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Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide, 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 40mM NaN3/1mM substrate for 8 hours at 293K., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.11 α = 90 b = 68.8 β = 90 c = 79.791 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 2.74 52 87.3 0.089 21.1 4.8 8970 -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) 2.75 2.85 49.3 0.41 1.7 3 502
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 2.74 52 8502 429 86.91 0.23994 0.23718 0.2279 0.29587 0.277 RANDOM 84.396
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] 1.13 -3.4 2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_4_deg 13.222 r_dihedral_angle_1_deg 5.473 r_angle_refined_deg 0.967 r_scangle_it 0.72 r_scbond_it 0.429 r_nbtor_refined 0.302 r_mcangle_it 0.275 r_nbd_refined 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.382 r_dihedral_angle_3_deg 14.214 r_dihedral_angle_4_deg 13.222 r_dihedral_angle_1_deg 5.473 r_angle_refined_deg 0.967 r_scangle_it 0.72 r_scbond_it 0.429 r_nbtor_refined 0.302 r_mcangle_it 0.275 r_nbd_refined 0.172 r_symmetry_hbond_refined 0.162 r_mcbond_it 0.143 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.099 r_metal_ion_refined 0.075 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 2393 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 26
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling