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Crystal structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 2-5 % PEG 10,000, 0.4-0.6 M lithium sulphate or 0.8-1 M sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.02 69.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.805 α = 90 b = 120.805 β = 90 c = 159.65 γ = 90
Symmetry Space Group I 41 2 2
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 MARRESEARCH 58 CM LONG, PT-COATED,FUSED SILICA, VERTICAL FOCUSMIRROR 2001-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.008 SSRL BL7-1
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 3 15 99 0.076 0.081 20.1 8.1 12157 12035 80.1
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 3 3.16 100 0.428 0.458 4.1 8.2 1729
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 1RM4 3 15 11522 11522 576 99.94 0.212 0.21236 0.20974 0.2791 0.26644 0.3268 RANDOM 33.196
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] -0.82 -0.82 1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.016 r_dihedral_angle_3_deg 18.855 r_dihedral_angle_4_deg 14.59 r_dihedral_angle_1_deg 7.11 r_scangle_it 1.698 r_angle_refined_deg 1.472 r_scbond_it 1.074 r_mcangle_it 0.867 r_mcbond_it 0.468 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.016 r_dihedral_angle_3_deg 18.855 r_dihedral_angle_4_deg 14.59 r_dihedral_angle_1_deg 7.11 r_scangle_it 1.698 r_angle_refined_deg 1.472 r_scbond_it 1.074 r_mcangle_it 0.867 r_mcbond_it 0.468 r_nbtor_refined 0.315 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.215 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2529 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing