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Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BE7 PDB ENTRY 3BE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 100MM SUCCINIC ACID PH 7.0, 15% PEG 3350, 5MM ZINC SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK TEMPERATURE 294K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.98 58.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.325 α = 90 b = 146.04 β = 90 c = 255.646 γ = 90
Symmetry Space Group P 21 21 21
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 315 MIRRORS 2007-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.62 50 99.4 0.11 0.11 4.1 3.6 127892 -0.5
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 2.62 2.71 98.4 0.79 0.7 3
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 3BE7 2.62 20 122571 3808 99.1 0.23106 0.23008 0.2332 0.26364 0.2665 RANDOM 75.913
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] -3.5 3.31 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.96 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 14.334 r_scangle_it 6.689 r_dihedral_angle_1_deg 5.944 r_scbond_it 4.099 r_mcangle_it 3.682 r_mcbond_it 2.259 r_angle_refined_deg 1.175 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.96 r_dihedral_angle_3_deg 17.842 r_dihedral_angle_4_deg 14.334 r_scangle_it 6.689 r_dihedral_angle_1_deg 5.944 r_scbond_it 4.099 r_mcangle_it 3.682 r_mcbond_it 2.259 r_angle_refined_deg 1.175 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.266 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.16 r_nbd_refined 0.141 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 24026 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 188
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling