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Crystal structure of human pyrroline-5-carboxylate reductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AG8 PDB ENTRY 2AG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20% PEG3350, 10% ETHYLENE GLYCOL 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE PH7.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.43 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.453 α = 90 b = 177.944 β = 106.7 c = 87.916 γ = 90
Symmetry Space Group C 1 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 CCD MARRESEARCH 2006-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.95 40 99.9 0.06 11.9 3.1 117744 25.5
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 1.95 2.06 99.9 0.38 2.3 2.6
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 2AG8 1.95 40 115902 1835 99.9 0.167 0.166 0.1702 0.19 0.1953 RANDOM 23.71
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] 0.79 0.28 1.6 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.597 r_dihedral_angle_4_deg 13.197 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 5.685 r_scangle_it 2.249 r_angle_other_deg 1.497 r_angle_refined_deg 1.455 r_scbond_it 1.404 r_mcangle_it 0.921 r_mcbond_it 0.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.597 r_dihedral_angle_4_deg 13.197 r_dihedral_angle_3_deg 12.712 r_dihedral_angle_1_deg 5.685 r_scangle_it 2.249 r_angle_other_deg 1.497 r_angle_refined_deg 1.455 r_scbond_it 1.404 r_mcangle_it 0.921 r_mcbond_it 0.556 r_symmetry_vdw_other 0.213 r_nbd_refined 0.199 r_nbd_other 0.186 r_symmetry_vdw_refined 0.176 r_nbtor_refined 0.16 r_chiral_restr 0.146 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.128 r_nbtor_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 9935 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 248
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing