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Crystal structure of P450 BM3 5F5 heme domain variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J4S PDB ENTRY 2J4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100-160 mM magnesium chloride, 100 mM 2-(N-morpholino)ethanesulfonic acid (pH 6.5), 10-20% PEG 3350/PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.01 α = 90 b = 148.37 β = 98.2 c = 64.15 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 MAR CCD 165 mm mirrors 2009-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 19.93 97.5 23.26 2.4 85590 83473 3.2 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.99 98.4
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 2J4S 1.9 19.93 85590 79299 4174 97.44 0.18358 0.18185 0.1822 0.21658 0.2165 RANDOM 28.418
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] -1.1 -0.73 0.48 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.608 r_dihedral_angle_4_deg 16.955 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 5.338 r_angle_refined_deg 1.959 r_chiral_restr 0.186 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.608 r_dihedral_angle_4_deg 16.955 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 5.338 r_angle_refined_deg 1.959 r_chiral_restr 0.186 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7242 Nucleic Acid Atoms Solvent Atoms 803 Heterogen Atoms 128
Software Software Software Name Purpose DNA data collection Auto-Rickshaw phasing REFMAC refinement XDS data reduction XSCALE data scaling