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Crystal Structure Analysis of the oxidized form of the M314I mutant of Peptidylglycine alpha-Hydroxylating Monooxygenase
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 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.479 α = 90 b = 66.458 β = 90 c = 70.049 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 CCD ADSC QUANTUM 4 mirrors 2003-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.7 48.2 87.6 0.041 0.041 8.8 2.5 61959 28704 2 2 41.7
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) 1 1.7 1.79 48.8 0.375 0.375 1.8 1.4 3006
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 (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 1.7 48.2 61959 25769 1377 86.99 0.20239 0.20239 0.2007 0.23261 RANDOM 41.687
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] 0.76 0.21 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 21.699 r_dihedral_angle_3_deg 16.302 r_dihedral_angle_1_deg 8.539 r_scangle_it 4.64 r_scbond_it 3.54 r_mcangle_it 2.352 r_angle_refined_deg 2.182 r_mcbond_it 2.023 r_angle_other_deg 1.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 21.699 r_dihedral_angle_3_deg 16.302 r_dihedral_angle_1_deg 8.539 r_scangle_it 4.64 r_scbond_it 3.54 r_mcangle_it 2.352 r_angle_refined_deg 2.182 r_mcbond_it 2.023 r_angle_other_deg 1.058 r_mcbond_other 0.432 r_symmetry_vdw_refined 0.383 r_symmetry_vdw_other 0.265 r_nbd_refined 0.235 r_nbd_other 0.214 r_xyhbond_nbd_refined 0.201 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.195 r_xyhbond_nbd_other 0.149 r_chiral_restr 0.148 r_nbtor_other 0.099 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2313 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing