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Structure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; glycerol cryo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 277 1.2 M NH4PO4, 0.3 M K2HPO4,
0.1 M NH4PO4 citrate (pH 4.2)
Crystal Properties Matthews coefficient Solvent content 3.45 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.7 α = 90 b = 109.7 β = 90 c = 93.9 γ = 120
Symmetry Space Group P 31 2 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 MARMOSAIC 225 mm CCD 2010-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9792 SLS X10SA
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 2.2 50 98.4 0.09 0.062 16.6 9.6 33006
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 2.3 95.5 0.4 5.5 10.3
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 3O1A 2.2 47.51 31857 1656 100 0.1922 0.19076 0.1864 0.22011 0.2145 RANDOM 36.062
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] -0.1 -0.05 -0.1 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.049 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_1_deg 5.083 r_scangle_it 2.032 r_scbond_it 1.236 r_angle_refined_deg 1.071 r_mcangle_it 0.747 r_mcbond_it 0.381 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.049 r_dihedral_angle_4_deg 17.626 r_dihedral_angle_3_deg 14.427 r_dihedral_angle_1_deg 5.083 r_scangle_it 2.032 r_scbond_it 1.236 r_angle_refined_deg 1.071 r_mcangle_it 0.747 r_mcbond_it 0.381 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_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 3239 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building PHASER phasing XSCALE data scaling