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Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JFL C-terminal domain in the intact structure of aspartate racemase from Pyrococcus horikoshii OT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.2 16% Peg8000, 0.10M MES, 0.2M Calcium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K
Crystal Properties Matthews coefficient Solvent content 1.97 37.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.829 α = 90 b = 45.328 β = 90 c = 57.366 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 2001-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.000 SPring-8 BL44B2
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 2.04 50 99.3 0.108 0.098 5.2 5.4 34260 34023 3 3 21.1
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 2.04 2.15 96.3 0.252 0.226 3 5.1 837
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT C-terminal domain in the intact structure of aspartate racemase from Pyrococcus horikoshii OT3 2.04 50 6491 6457 334 99.4 0.225 0.225 0.267 RANDOM 23.2
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] 1.91 -5.71 3.8
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_scangle_it 3.38 c_scbond_it 2.27 c_mcangle_it 2.2 c_mcbond_it 1.42 c_angle_deg 1.1 c_improper_angle_d 0.73 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 850 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing CNS refinement CCP4 data scaling