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Crystal structure of human phytanoyl-CoA dioxygenase PHYHD1 (apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model built from sulfur SAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 7% PEG3350, 200mM Calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.97 α = 90 b = 91.97 β = 90 c = 81.61 γ = 120
Symmetry Space Group P 31 2 1
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 MARMOSAIC 225 mm CCD 2006-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.95520 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 40.06 99 0.12 10 7 31832 31832 22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 92.5 2.24 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Model built from sulfur SAD data 1.9 40.06 29892 29892 1585 99.06 0.22108 0.22108 0.2191 0.2266 0.25793 0.2588 RANDOM 17.811
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] 0.95 0.47 0.95 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_4_deg 21.689 r_dihedral_angle_3_deg 15.772 r_scangle_it 8.866 r_scbond_it 6.755 r_dihedral_angle_1_deg 6.637 r_mcangle_it 4.214 r_mcbond_it 3.261 r_angle_refined_deg 1.569 r_angle_other_deg 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_4_deg 21.689 r_dihedral_angle_3_deg 15.772 r_scangle_it 8.866 r_scbond_it 6.755 r_dihedral_angle_1_deg 6.637 r_mcangle_it 4.214 r_mcbond_it 3.261 r_angle_refined_deg 1.569 r_angle_other_deg 0.941 r_mcbond_other 0.92 r_symmetry_vdw_refined 0.573 r_symmetry_vdw_other 0.263 r_nbd_refined 0.205 r_nbd_other 0.201 r_nbtor_refined 0.191 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.094 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XDS data scaling PHASER phasing