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Structure of human putative dehydrogenase MGC4172 in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EDO PDB entry 1EDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 100mM Bis-Tris pH 5.5, 200mM Ammonium Acetate, 2% Glycerol (total 7%), 18% PEG 3350, 0.5mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.71 α = 90 b = 124.669 β = 97.23 c = 75.13 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 2004-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.53 41.56 97.05 0.087 0.087 13 5.3 149996 145577 14.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.57 81.2 0.558 0.558 1.6 1.6 8970
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 PDB entry 1EDO 1.53 41.56 145565 143645 1920 97.05 0.16226 0.16226 0.1617 0.164 0.20638 0.2049 RANDOM 19.172
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] 1.18 0.27 -0.86 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 11.995 r_dihedral_angle_1_deg 5.568 r_scangle_it 3.617 r_scbond_it 2.411 r_angle_refined_deg 1.648 r_mcangle_it 1.448 r_mcbond_it 0.941 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 18.135 r_dihedral_angle_3_deg 11.995 r_dihedral_angle_1_deg 5.568 r_scangle_it 3.617 r_scbond_it 2.411 r_angle_refined_deg 1.648 r_mcangle_it 1.448 r_mcbond_it 0.941 r_nbtor_refined 0.306 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.14 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7549 Nucleic Acid Atoms Solvent Atoms 859 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing