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Crystal structure of apo wild type peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide (peptide not observed)
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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.099 α = 90 b = 65.93 β = 90 c = 69.809 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 PIXEL DECTRIS PILATUS3 2M 2016-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50 99.2 0.075 0.082 0.034 15.2 5.5 11068
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 2.4 2.44 88.1 0.329 0.405 0.232 0.843 2.6
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 FOURIER SYNTHESIS THROUGHOUT 1PHM 2.4 47.93 10468 562 99.07 0.2039 0.1997 0.233 0.2811 0.2706 RANDOM 51.291
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] -1.15 2.73 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.875 r_dihedral_angle_3_deg 19.311 r_dihedral_angle_4_deg 17.556 r_dihedral_angle_1_deg 8.658 r_angle_refined_deg 1.933 r_angle_other_deg 1.129 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.875 r_dihedral_angle_3_deg 19.311 r_dihedral_angle_4_deg 17.556 r_dihedral_angle_1_deg 8.658 r_angle_refined_deg 1.933 r_angle_other_deg 1.129 r_chiral_restr 0.116 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 27 Heterogen Atoms
Software Software Software Name Purpose DENZO data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing