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Crystal structure of V57P mutant of human cystatin C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G96 PDB ENTRY 1G96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M Imidazole pH=6.5
0.9M Sodium acetate,
additive 2.0M NDSB-221, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.29 71.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.135 α = 90 b = 140.135 β = 90 c = 140.135 γ = 90
Symmetry Space Group I 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2010-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97923 APS 19-BM
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 2.26 50 99.8 0.088 36.5 14 11234 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.3 2.16 12.5
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 1G96 2.26 27.48 10697 537 99.35 0.18869 0.18667 0.1982 0.2289 0.2467 RANDOM 46.279
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.882 r_dihedral_angle_4_deg 25.564 r_dihedral_angle_3_deg 17.23 r_scangle_it 12.602 r_scbond_it 9.689 r_dihedral_angle_1_deg 5.77 r_mcangle_it 5.187 r_mcbond_it 3.815 r_angle_refined_deg 1.657 r_angle_other_deg 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.882 r_dihedral_angle_4_deg 25.564 r_dihedral_angle_3_deg 17.23 r_scangle_it 12.602 r_scbond_it 9.689 r_dihedral_angle_1_deg 5.77 r_mcangle_it 5.187 r_mcbond_it 3.815 r_angle_refined_deg 1.657 r_angle_other_deg 0.323 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 871 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 44
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling