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Crystal structure of alanine dehydrogenase-like protein from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2M Magnesium formate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.61 52.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.06 α = 90 b = 86.06 β = 90 c = 178.203 γ = 120
Symmetry Space Group P 63 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 95 PIXEL DECTRIS PILATUS3 S 2M 2019-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 46.5 100 0.128 0.131 0.03 0.999 18.1 19 14250
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 0.857 0.88 0.196 0.967 19.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 46.5 13520 696 99.94 0.22812 0.22517 0.2257 0.28578 0.2857 RANDOM 57.067
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] 1.86 0.93 1.86 -6.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.426 r_dihedral_angle_4_deg 20.028 r_dihedral_angle_3_deg 18.416 r_dihedral_angle_1_deg 5.772 r_long_range_B_refined 4.485 r_long_range_B_other 4.481 r_mcangle_it 2.658 r_mcangle_other 2.657 r_scangle_other 2.46 r_mcbond_other 1.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.426 r_dihedral_angle_4_deg 20.028 r_dihedral_angle_3_deg 18.416 r_dihedral_angle_1_deg 5.772 r_long_range_B_refined 4.485 r_long_range_B_other 4.481 r_mcangle_it 2.658 r_mcangle_other 2.657 r_scangle_other 2.46 r_mcbond_other 1.535 r_mcbond_it 1.534 r_scbond_it 1.39 r_scbond_other 1.39 r_angle_refined_deg 1.231 r_angle_other_deg 1.043 r_chiral_restr 0.041 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2500 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction