☰ Navigation Tabs
The Crystal Structure of RALDH1 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M CaCl2, 0.1M MgCl2, 0.1M PIPES pH7, 22.5% PEG smear
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.343 α = 90 b = 149.56 β = 95.428 c = 125.076 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2022-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95374 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.5 48.16 98.5 0.95 4.7 3 46102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.62 0.618
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.5 48.16 46082 2196 98.283 0.231 0.2302 0.2321 0.2543 0.2524 64.069
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 5.759 -3.753 -0.466 -4.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.684 r_dihedral_angle_6_deg 10.535 r_dihedral_angle_1_deg 5.07 r_lrange_it 4.8 r_lrange_other 4.8 r_mcangle_it 2.655 r_mcangle_other 2.655 r_dihedral_angle_2_deg 2.6 r_scangle_it 2.287 r_scangle_other 2.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.684 r_dihedral_angle_6_deg 10.535 r_dihedral_angle_1_deg 5.07 r_lrange_it 4.8 r_lrange_other 4.8 r_mcangle_it 2.655 r_mcangle_other 2.655 r_dihedral_angle_2_deg 2.6 r_scangle_it 2.287 r_scangle_other 2.287 r_mcbond_it 1.518 r_mcbond_other 1.518 r_scbond_it 1.263 r_scbond_other 1.263 r_angle_refined_deg 0.667 r_angle_other_deg 0.239 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_other 0.206 r_symmetry_nbd_refined 0.204 r_nbd_refined 0.174 r_symmetry_nbd_other 0.169 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_5 0.055 r_ncsr_local_group_7 0.051 r_ncsr_local_group_11 0.051 r_ncsr_local_group_26 0.051 r_symmetry_xyhbond_nbd_other 0.05 r_ncsr_local_group_13 0.05 r_ncsr_local_group_22 0.05 r_ncsr_local_group_1 0.049 r_ncsr_local_group_23 0.049 r_ncsr_local_group_27 0.049 r_ncsr_local_group_4 0.048 r_ncsr_local_group_12 0.048 r_ncsr_local_group_18 0.048 r_ncsr_local_group_25 0.048 r_ncsr_local_group_6 0.047 r_ncsr_local_group_20 0.047 r_ncsr_local_group_24 0.047 r_ncsr_local_group_17 0.046 r_ncsr_local_group_3 0.045 r_ncsr_local_group_10 0.045 r_ncsr_local_group_16 0.045 r_ncsr_local_group_2 0.044 r_ncsr_local_group_9 0.044 r_ncsr_local_group_21 0.044 r_ncsr_local_group_19 0.043 r_ncsr_local_group_28 0.043 r_ncsr_local_group_15 0.042 r_ncsr_local_group_8 0.041 r_ncsr_local_group_14 0.039 r_chiral_restr 0.031 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30496 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 356
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing