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Rat STEAP4 oxidoreductase domain complexed with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VQ3 PDB ENTRY 2VQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M BIS-TRIS HCL PH 5.5; 2.1 M AMMONIUM SULFATE; 0.001M NADPH.
Crystal Properties Matthews coefficient Solvent content 2.07 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.228 α = 90 b = 85.111 β = 90 c = 128.035 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 CCD 2011-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 2.2 50 99.1 0.1 7.9 7.8 39044 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 94.8 0.46 2.8 6.4
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 2VQ3 2.2 37 36854 1948 99.16 0.20471 0.20285 0.2116 0.23784 0.2473 RANDOM 34.747
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] -0.28 2.79 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.48 r_dihedral_angle_4_deg 14.873 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.103 r_scangle_it 4.545 r_angle_other_deg 3.897 r_scbond_it 2.873 r_mcangle_it 1.91 r_angle_refined_deg 1.861 r_mcbond_it 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.48 r_dihedral_angle_4_deg 14.873 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 6.103 r_scangle_it 4.545 r_angle_other_deg 3.897 r_scbond_it 2.873 r_mcangle_it 1.91 r_angle_refined_deg 1.861 r_mcbond_it 0.985 r_symmetry_vdw_other 0.368 r_symmetry_vdw_refined 0.312 r_nbd_other 0.233 r_nbd_refined 0.211 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_other 0.126 r_nbtor_other 0.105 r_chiral_restr 0.099 r_bond_refined_d 0.021 r_mcbond_other 0.021 r_gen_planes_other 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5292 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MrBUMP phasing