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Oxidized Peptidylglycine Alpha-Hydroxylating Monooxygenase (PHM) in a New Crystal Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OPM PDB ENTRY 1OPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 4000, magnesium chloride, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.523 α = 90 b = 65.683 β = 90 c = 69.871 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 30.01 92.9 0.058 0.058 12.04 4.7 14064 14064 -3.7 38.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32 100 0.444 0.444 2.18 4.7 2026
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OPM 2.2 30.01 2 14034 14034 687 98.908 0.192 0.192 0.1895 0.2389 RANDOM 38.582
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] -2.59 2.739 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 17.949 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 8.542 r_scangle_it 3.173 r_scbond_it 2.205 r_angle_refined_deg 1.822 r_mcangle_it 1.383 r_scangle_other 1.309 r_mcbond_it 1.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.563 r_dihedral_angle_4_deg 17.949 r_dihedral_angle_3_deg 17.266 r_dihedral_angle_1_deg 8.542 r_scangle_it 3.173 r_scbond_it 2.205 r_angle_refined_deg 1.822 r_mcangle_it 1.383 r_scangle_other 1.309 r_mcbond_it 1.121 r_angle_other_deg 0.913 r_scbond_other 0.876 r_mcangle_other 0.632 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.213 r_mcbond_other 0.21 r_symmetry_hbond_refined 0.208 r_nbd_other 0.195 r_symmetry_vdw_other 0.189 r_nbtor_refined 0.188 r_symmetry_vdw_refined 0.136 r_chiral_restr 0.113 r_nbtor_other 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2425 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 2
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling AMoRE phasing