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Crystal structure of human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDS) complex with NAD, a binary form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H9E PDB ENTRY 3H9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 277.15 20% PEG 3350, 0.2 M Na2SO4, 10% ethylene glycol and 0.1 M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.61 α = 90 b = 71.86 β = 123.32 c = 81.1 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2009-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 2.15 67.77 94.1 0.171 7 5.3 35287 27.6
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 2.15 2.27 92 0.671 2.3 5.3
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 (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 3H9E 2.15 67.77 35287 33519 1768 93.7 0.17 0.168 0.1679 0.222 0.2214 RANDOM 24.02
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] 0.72 -0.47 -0.51 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.952 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 6.647 r_angle_refined_deg 1.54 r_angle_other_deg 0.958 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.952 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 13.677 r_dihedral_angle_1_deg 6.647 r_angle_refined_deg 1.54 r_angle_other_deg 0.958 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5138 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 118
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling