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Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite, obtained in the presence of substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PHM PDB ENTRY 1PHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 1mM substrate (Ac-3,5-diI-YG) for 1 hour and then soaked in 300mM NaNO2/1mM substrate for 14 hours at 293K., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.356 α = 90 b = 68.783 β = 90 c = 79.979 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 MAR scanner 345 mm plate 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.98 NSLS X4C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 52 99 0.085 35.7 7 10776 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 91.4 0.53 2.1 5.6 970
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 PDB ENTRY 1PHM 2.7 52 10216 518 98.86 0.22387 0.22146 0.2089 0.27236 0.2561 RANDOM 60.565
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] 0.56 -3.61 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 15.739 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_1_deg 6.474 r_scangle_it 1.496 r_angle_refined_deg 1.221 r_scbond_it 0.957 r_mcangle_it 0.674 r_mcbond_it 0.416 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.537 r_dihedral_angle_3_deg 15.739 r_dihedral_angle_4_deg 15.181 r_dihedral_angle_1_deg 6.474 r_scangle_it 1.496 r_angle_refined_deg 1.221 r_scbond_it 0.957 r_mcangle_it 0.674 r_mcbond_it 0.416 r_nbtor_refined 0.311 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_metal_ion_refined 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2410 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 15
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling