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Crystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V3V 1V3V.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 PEG3350, NaI, ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 56.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.543 α = 90 b = 92.543 β = 90 c = 202.77 γ = 90
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 2005-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.98402 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 2.3 67.57 99.4 0.139 74944 74944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.42 97.1
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 1V3V.pdb 2.3 62.3 72302 72302 1920 98.42 0.1969 0.1969 0.19511 0.2248 0.24933 0.2395 RANDOM 43.497
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] -0.55 -0.55 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.289 r_dihedral_angle_3_deg 16.573 r_dihedral_angle_4_deg 15.973 r_dihedral_angle_1_deg 7.384 r_scangle_it 7.035 r_scbond_it 5.181 r_mcangle_it 2.905 r_mcbond_it 1.991 r_angle_refined_deg 1.618 r_angle_other_deg 0.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.289 r_dihedral_angle_3_deg 16.573 r_dihedral_angle_4_deg 15.973 r_dihedral_angle_1_deg 7.384 r_scangle_it 7.035 r_scbond_it 5.181 r_mcangle_it 2.905 r_mcbond_it 1.991 r_angle_refined_deg 1.618 r_angle_other_deg 0.843 r_mcbond_other 0.523 r_nbd_refined 0.19 r_nbtor_refined 0.175 r_nbd_other 0.169 r_symmetry_vdw_other 0.159 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.088 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9834 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing