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Methanococcus jannaschii serine hydroxymethyl-transferase, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KL2 PDB ENTRY 1KL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 NAH2PO4/K2HPO4 1.8 M, PH 5.0
Crystal Properties Matthews coefficient Solvent content 2.74 55.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.594 α = 90 b = 110.158 β = 90 c = 110.689 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 100 CCD ADSC QUANTUM 315r M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.85 50 98.5 0.08 13.93 5.9 25528 -3
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 2.85 2.95 98.9 0.5 2.53 5.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1KL2 2.83 50 24195 1293 97.9 0.24474 0.24209 0.2432 0.29768 0.2957 RANDOM 85.509
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] -2.94 -1.51 4.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_4_deg 19.986 r_dihedral_angle_3_deg 18.631 r_dihedral_angle_1_deg 4.984 r_angle_refined_deg 0.992 r_scangle_it 0.753 r_scbond_it 0.421 r_mcangle_it 0.417 r_mcbond_it 0.223 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.013 r_dihedral_angle_4_deg 19.986 r_dihedral_angle_3_deg 18.631 r_dihedral_angle_1_deg 4.984 r_angle_refined_deg 0.992 r_scangle_it 0.753 r_scbond_it 0.421 r_mcangle_it 0.417 r_mcbond_it 0.223 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 6391 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing