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Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite
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, 1.25 mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 5mM ascorbic acid and then soaked in 300mM NaNO2 (with 5mM ascorbic acid) for 13 hours at RT., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.973 α = 90 b = 69.317 β = 90 c = 81.114 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 2007-11-17 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 3.1 53 99.9 0.081 23.4 7 7468 -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) 3.1 3.21 99 0.57 2.2 6 715
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 3.1 52.7 7090 344 99.68 0.2187 0.2156 0.2037 0.28204 0.2639 RANDOM 62.927
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] -3.51 1.23 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_3_deg 16.967 r_dihedral_angle_4_deg 12.888 r_dihedral_angle_1_deg 6.326 r_scangle_it 1.159 r_angle_refined_deg 1.112 r_scbond_it 0.71 r_mcangle_it 0.53 r_nbtor_refined 0.307 r_mcbond_it 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.41 r_dihedral_angle_3_deg 16.967 r_dihedral_angle_4_deg 12.888 r_dihedral_angle_1_deg 6.326 r_scangle_it 1.159 r_angle_refined_deg 1.112 r_scbond_it 0.71 r_mcangle_it 0.53 r_nbtor_refined 0.307 r_mcbond_it 0.301 r_symmetry_vdw_refined 0.235 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.125 r_metal_ion_refined 0.09 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.077 r_bond_refined_d 0.009 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 2388 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 8
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling