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NADP complex of Pyrroline-5-carboxylate reductase from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 Ammonium sulfate, HEPES, PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.6 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.701 α = 90 b = 49.826 β = 90 c = 65.445 γ = 90
Symmetry Space Group P 21 21 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 CUSTOM-MADE 2004-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97917 APS 19-ID
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 2.1 50 78.4 0.086 14.1 2.7 17930 14057 -3
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 2.1 2.18 35.2 0.391 1.72 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1YQG 2.1 50 14047 14047 717 78.74 0.18099 0.18099 0.17715 0.1805 0.25244 0.1861 RANDOM 41.854
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] -0.84 -0.26 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 20.131 r_dihedral_angle_3_deg 18.204 r_dihedral_angle_1_deg 6.831 r_scangle_it 5.156 r_scbond_it 3.776 r_angle_refined_deg 1.937 r_mcangle_it 1.708 r_mcbond_it 1.17 r_symmetry_hbond_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.423 r_dihedral_angle_4_deg 20.131 r_dihedral_angle_3_deg 18.204 r_dihedral_angle_1_deg 6.831 r_scangle_it 5.156 r_scbond_it 3.776 r_angle_refined_deg 1.937 r_mcangle_it 1.708 r_mcbond_it 1.17 r_symmetry_hbond_refined 0.303 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 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 1980 Nucleic Acid Atoms Solvent Atoms 241 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MERLOT phasing