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Crystal Structure of T.th.HB8 Serine Hydroxymethyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKJ PDB ENTRY 1KKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.8M lithium sulfate, 0.4M ammonium sulfate, 0.1M sodium citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.988 α = 90 b = 82.884 β = 91.67 c = 94.074 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 MAR CCD 165 mm 2004-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.75 SPring-8 BL41XU
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 1.15 53.5 95.8 302432 302432 6.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.19 90.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1KKJ 1.15 42 2 302432 299961 29947 95.2 0.18 0.18 0.1798 0.19 0.1901 RANDOM 11.9
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] -0.63 -0.13 -0.04 0.67
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scbond_it 14.03 c_scangle_it 6.3 c_angle_deg 1.3 c_mcangle_it 1.07 c_improper_angle_d 1.05 c_mcbond_it 0.73 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6141 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 40
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing