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Peptidylglycine alpha hydroxylating monooxygenase, Q272E
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 = 39.166 α = 85.03 b = 53.535 β = 89.79 c = 86.139 γ = 77.62
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 PILATUS3 6M 2021-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.05 38.25 98.1 0.071 0.076 0.025 0.999 15.9 8.9 41882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.11 96.8 0.539 0.574 0.194 0.95 3.5 8.7
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 1phm 2.05 38.25 39833 2063 98.07 0.198 0.1959 0.205 0.2392 0.2407 RANDOM 43.646
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] -0.05 0.03 -0.02 -0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.833 r_dihedral_angle_3_deg 18.064 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_1_deg 8.252 r_angle_refined_deg 1.701 r_angle_other_deg 1.271 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.833 r_dihedral_angle_3_deg 18.064 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_1_deg 8.252 r_angle_refined_deg 1.701 r_angle_other_deg 1.271 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4836 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 16
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing