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Crystal Structure of Human Renin Complexed with Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I4Q PDB code 2I4Q, molecule A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 10-20% PEG 3350, 50 mM sodium citrate pH 4.5, 0.6 M NaCl. Renin concentration 8-12 mg/mL., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.13 60.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.885 α = 90 b = 140.885 β = 90 c = 140.885 γ = 90
Symmetry Space Group P 21 3
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 210 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 50 96 0.063 0.063 16.98 3.08 70222
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 1.9 1.97 88 0.606 1.01 2.2 6373
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 code 2I4Q, molecule A 1.9 20 70170 3528 96.07 0.196 0.194 0.2191 0.229 0.2472 RANDOM 30.946
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 34.454 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 7.101 r_scangle_it 2.074 r_scbond_it 1.427 r_angle_refined_deg 1.274 r_mcangle_it 0.961 r_angle_other_deg 0.95 r_mcbond_it 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.454 r_dihedral_angle_4_deg 21.057 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 7.101 r_scangle_it 2.074 r_scbond_it 1.427 r_angle_refined_deg 1.274 r_mcangle_it 0.961 r_angle_other_deg 0.95 r_mcbond_it 0.841 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.193 r_nbd_other 0.187 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.142 r_mcbond_other 0.118 r_chiral_restr 0.1 r_nbtor_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5165 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing