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Rap2a protein (SMA2265) from Serratia marcescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B6I PDB ENTRY 4B6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 SITTING DROP VAPOUR DIFFUSION. PROTEIN BUFFER: 10 MM SODIUM PHOSPHATE, PH 6.4 RESERVOIR CONDITION: 25% W/V POLYETHYLENE GLYCOL 1000, 0.1 M MES, PH6.5. CRYOPROTECTANT USED: 20% GLYCEROL WITH MOTHER LIQUOR.
Crystal Properties Matthews coefficient Solvent content 2.06 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.65 α = 90 b = 81.35 β = 91.54 c = 58.45 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 287 PIXEL DECTRIS PILATUS 6M KIRKPATRICK BAEZ BIMORPH MIRROR PAIR 2012-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 40.6 99.4 0.1 15.3 7.4 29067 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.9 0.52 4 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4B6I 1.9 58.43 27568 1477 99.25 0.18566 0.18306 0.1828 0.23358 0.2325 RANDOM 23.721
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] 0.23 0.62 -0.37 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.7 r_dihedral_angle_3_deg 17.708 r_dihedral_angle_4_deg 9.856 r_dihedral_angle_1_deg 5.517 r_angle_refined_deg 1.745 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.7 r_dihedral_angle_3_deg 17.708 r_dihedral_angle_4_deg 9.856 r_dihedral_angle_1_deg 5.517 r_angle_refined_deg 1.745 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2926 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing