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Crystal structure of a single mutant (N71D) of triosephosphate isomerase from human
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JK2 PDB ENTRY 2JK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 PROTEIN WAS CRYSTALLIZED FROM: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4,000
Crystal Properties Matthews coefficient Solvent content 2.3 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.943 α = 90 b = 72.841 β = 90 c = 93.302 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 90 CCD MARRESEARCH MIRRORS 2010-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F APS 21-ID-F
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 1.5 39.28 99.7 0.06 7.2 2 71346 1
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 1.5 1.54 98.6 0.49 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2JK2 1.5 39.28 67516 3603 99.47 0.2001 0.19873 0.22564 0.2263 RANDOM 18.537
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.777 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_4_deg 10.686 r_dihedral_angle_1_deg 5.149 r_scangle_it 4.928 r_scbond_it 3.266 r_mcangle_it 2.897 r_mcbond_it 2.15 r_angle_refined_deg 1.025 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.777 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_4_deg 10.686 r_dihedral_angle_1_deg 5.149 r_scangle_it 4.928 r_scbond_it 3.266 r_mcangle_it 2.897 r_mcbond_it 2.15 r_angle_refined_deg 1.025 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_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 3712 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing