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A polymorph of carboxypeptidase B zymogen structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NSA PDB ENTRY 1NSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 0.1M sodium citrate, 1.6M ammonium sulfate, pH5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.59 α = 109.94 b = 49.97 β = 104.5 c = 50.63 γ = 96.19
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 MAR CCD 165 mm 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
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 1.88 30 96.4 0.05 0.058 35004 33758 2 -3 23.476
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 1.89 1.93 88.3 0.222 5.2
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 (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 1NSA 1.89 19.63 33758 33081 676 100 0.16648 0.16583 0.163 0.19816 0.1962 RANDOM 16.811
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] 0.08 0.4 0.56 0.56 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 14.483 r_dihedral_angle_3_deg 11.545 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.966 r_scbond_it 1.755 r_mcangle_it 1.052 r_angle_refined_deg 1.025 r_mcbond_it 0.531 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 14.483 r_dihedral_angle_3_deg 11.545 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.966 r_scbond_it 1.755 r_mcangle_it 1.052 r_angle_refined_deg 1.025 r_mcbond_it 0.531 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg 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 3189 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 31
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction