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Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V93 PDB ENTRY 1V93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris-HCl, 0.2M Ammonium Sulfate, 20-25% PEG 4000, 5% GLYCEROL , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.588 α = 90 b = 90.93 β = 90 c = 125.152 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 210r 2010-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.57 19.96 91.54 72447
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 1V93 2.8 19.96 57531 3050 93.85 0.20869 0.2039 0.2025 0.30586 0.2913 RANDOM 19.499
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] 0.07 -0.03 -0.05 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.402 r_dihedral_angle_3_deg 20.35 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_1_deg 6.256 r_scangle_it 3.262 r_scbond_it 1.851 r_angle_refined_deg 1.572 r_mcangle_it 1.218 r_mcbond_it 0.618 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.402 r_dihedral_angle_3_deg 20.35 r_dihedral_angle_4_deg 19.742 r_dihedral_angle_1_deg 6.256 r_scangle_it 3.262 r_scbond_it 1.851 r_angle_refined_deg 1.572 r_mcangle_it 1.218 r_mcbond_it 0.618 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18416 Nucleic Acid Atoms Solvent Atoms 909 Heterogen Atoms 430
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction HKL-2000 data scaling