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Peptidylglycine alpha hydroxylating monoxygenase, Q272A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 Hampton Research Cryschem 24-well plates. 1.5 uL of WT PHM protein at 17 mg/mL in 20 mM sodium phosphate, pH 7.5 was added to 1.5 uL of mother liquor solution containing 16-18% PEG 20K, 20-250 mM sodium citrate, and 2 mM CuSO4. Plates were sealed using transparent tape. Crystals were formed within one week, and these initial crystals were used to seed succeeding trays using the same crystal conditions. Seeding was performed using a Hampton Research seed bead and Hampton Research seeding tool. Initial crystals (5-7 crystals) were vortexed with seed beads for 30 seconds in 30 uL mother liquor, and streaked into a new drop using the seeding tool.
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.878 α = 84.71 b = 53.488 β = 89.82 c = 86.056 γ = 77.96
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.00 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 38.05 95.4 0.438 6 15.5 43540
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 90.2 0.143 10.9
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 1phm 2.8 38.05 15589 835 98.9 0.2033 0.1984 0.2085 0.2964 0.2939 RANDOM 43.221
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] 0.03 -0.03 -0.04 -0.02 -0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_3_deg 19.776 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_1_deg 9.464 r_angle_refined_deg 1.61 r_angle_other_deg 1.169 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_dihedral_angle_3_deg 19.776 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_1_deg 9.464 r_angle_refined_deg 1.61 r_angle_other_deg 1.169 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing