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Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 19-24% PEG 4000, Tris HCL
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.123 α = 90 b = 69.845 β = 90 c = 81.992 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 CMOS RDI CMOS_8M 2013-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.65 53.17 79 0.076 0.093 0.052 0.996 10.1 2.7 9451
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.78 69.3 0.907 1.107 0.623 0.428 2.5
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 1PHM 2.98 53.17 7507 372 92.28 0.1836 0.1797 0.1836 0.2606 0.2568 RANDOM 84.506
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] -3.6 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 16.935 r_dihedral_angle_1_deg 7.351 r_angle_refined_deg 1.463 r_angle_other_deg 0.924 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_4_deg 18.022 r_dihedral_angle_3_deg 16.935 r_dihedral_angle_1_deg 7.351 r_angle_refined_deg 1.463 r_angle_other_deg 0.924 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2413 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction Coot model building REFMAC phasing XDS data reduction