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Structure of cytochrome P450 EryK in complex with its natural substrate erD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJN PDB ENTRY 2JJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 25% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M TRIS PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.05 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.84 α = 90 b = 36.526 β = 93.92 c = 96.004 γ = 90
Symmetry Space Group P 1 21 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 ADSC CCD 2007-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 30 91.5 0.06 13 4 27953 2
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 2.15 80.4 0.24 10.9 3.1
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 2JJN 1.99 95.78 24282 1281 91.5 0.167 0.163 0.1686 0.227 0.2332 RANDOM 23.2
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] -1.21 -0.54 0.06 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 15.329 r_dihedral_angle_1_deg 5.71 r_scangle_it 3.295 r_scbond_it 2.302 r_angle_refined_deg 1.577 r_mcangle_it 1.439 r_angle_other_deg 1.211 r_mcbond_it 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 18.496 r_dihedral_angle_3_deg 15.329 r_dihedral_angle_1_deg 5.71 r_scangle_it 3.295 r_scbond_it 2.302 r_angle_refined_deg 1.577 r_mcangle_it 1.439 r_angle_other_deg 1.211 r_mcbond_it 0.893 r_nbtor_refined 0.305 r_nbd_other 0.257 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.193 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.148 r_nbtor_other 0.126 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_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_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 3050 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing