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Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound carbon monooxide (CO)
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. Then, CO-soaking in a pressure chamber at 3 atm of CO for 15 minutes at RT., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.246 α = 90 b = 69.715 β = 90 c = 83.121 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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25
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 35 97 0.08 4.6 5.9 37462 -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 2.05 100 0.41 1.5 6.7
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 34.63 26400 1397 99.88 0.20822 0.20678 0.1986 0.23539 0.2232 RANDOM 40.018
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] -0.39 0.24 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 6.146 r_scangle_it 1.837 r_scbond_it 1.211 r_angle_refined_deg 1.102 r_mcangle_it 0.69 r_mcbond_it 0.362 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 14.28 r_dihedral_angle_1_deg 6.146 r_scangle_it 1.837 r_scbond_it 1.211 r_angle_refined_deg 1.102 r_mcangle_it 0.69 r_mcbond_it 0.362 r_nbtor_refined 0.3 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.157 r_metal_ion_refined 0.133 r_xyhbond_nbd_refined 0.095 r_symmetry_hbond_refined 0.095 r_chiral_restr 0.078 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 2418 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 29
Software Software Software Name Purpose CBASS data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling