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Crystal structure of the P450cam G248T mutant in the cyanide bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKD PDB entry 1akd
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 1 UL OF 15 MG/ML P450 IN 50 MM Potassium phosphate, 250 MM KCL WERE MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION
(100 mM Tris, 250 mM KCl, 27-30% PEG 8000, 100 MM DTE), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.8 α = 90 b = 64.6 β = 90 c = 105.5 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 MARRESEARCH DYNAMICALLY BENDABLE MIRROR 2007-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9796 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 20 99 0.055 19.1 5.5 40676 40676 -3
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) 1.8 1.9 95 0.425 3.5 4.8
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1akd 1.8 19.94 40675 38641 2034 100 0.1785 0.17627 0.175 0.22045 0.219 RANDOM 24.505
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] 0.95 0.54 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.383 r_dihedral_angle_3_deg 14.497 r_dihedral_angle_4_deg 12.967 r_dihedral_angle_1_deg 5.781 r_scangle_it 3.946 r_scbond_it 2.503 r_angle_refined_deg 1.554 r_mcangle_it 1.453 r_mcbond_it 0.771 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.383 r_dihedral_angle_3_deg 14.497 r_dihedral_angle_4_deg 12.967 r_dihedral_angle_1_deg 5.781 r_scangle_it 3.946 r_scbond_it 2.503 r_angle_refined_deg 1.554 r_mcangle_it 1.453 r_mcbond_it 0.771 r_nbtor_refined 0.306 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.147 r_symmetry_hbond_refined 0.132 r_metal_ion_refined 0.118 r_chiral_restr 0.115 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_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 3215 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling CNS phasing