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Crystal structure of the CLIP-170 CAP-Gly domain 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.937 α = 90 b = 54.937 β = 90 c = 57.27 γ = 120
Symmetry Space Group P 32 2 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 IMAGE PLATE MAC Science DIP-2040 2004-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.45 50 98.9 0.042 44.3 17953
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 1.56 100 0.107 11.5
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 1LPL 1.45 47.67 17032 915 98.97 0.19281 0.19168 0.1904 0.21483 0.2035 RANDOM 22.472
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] -0.22 -0.11 -0.22 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.725 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 14.253 r_dihedral_angle_1_deg 6.281 r_scangle_it 3.574 r_scbond_it 2.464 r_mcangle_it 1.849 r_angle_refined_deg 1.356 r_mcbond_it 1.221 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.725 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 14.253 r_dihedral_angle_1_deg 6.281 r_scangle_it 3.574 r_scbond_it 2.464 r_mcangle_it 1.849 r_angle_refined_deg 1.356 r_mcbond_it 1.221 r_nbtor_refined 0.31 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.157 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 651 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing