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Human Cytochrome P450 2A13 in complex with Pilocarpine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FDV PDB ENTRY 2FDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 30% PEG 3350, 0.175 M Tris, pH 8.5, and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.501 α = 101.01 b = 119.862 β = 101.72 c = 154.871 γ = 93.59
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 MARMOSAIC 325 mm CCD RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR 2010-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 3 117 98.3 0.117 0.135 9.4 4 96716
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 3 3.16 97.9 0.635 2.1 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 2FDV 3 102.88 91882 91882 4826 98.3 0.218 0.213 0.2172 0.303 0.2931 RANDOM 58.19
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] -0.05 -0.02 0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_3_deg 21.501 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_1_deg 6.975 r_scangle_it 2.289 r_angle_refined_deg 1.786 r_scbond_it 1.408 r_mcangle_it 1.029 r_mcbond_it 0.551 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.947 r_dihedral_angle_3_deg 21.501 r_dihedral_angle_4_deg 19.387 r_dihedral_angle_1_deg 6.975 r_scangle_it 2.289 r_angle_refined_deg 1.786 r_scbond_it 1.408 r_mcangle_it 1.029 r_mcbond_it 0.551 r_chiral_restr 0.111 r_bond_refined_d 0.017 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 30017 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 434
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling