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Methanococcus jannaschii TBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MP9 PDB entry 1MP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG MME 2000, sodium acetate, ammonium sulfate, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.242 α = 90 b = 55.532 β = 91.05 c = 123.434 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 95 CCD ADSC QUANTUM 315 2004-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97910 Photon Factory BL-5A
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 1.9 62 99.9 0.039 9.2 57094 57094
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 1.9 2 99.9 0.35 2.1
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 1MP9 1.9 50 54183 2892 100 0.22734 0.22557 0.2246 0.25911 0.2568 RANDOM 39.653
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] -0.54 -0.13 1.64 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.592 r_dihedral_angle_4_deg 23.135 r_dihedral_angle_3_deg 16.133 r_dihedral_angle_1_deg 5.371 r_scangle_it 2.948 r_scbond_it 1.826 r_angle_refined_deg 1.29 r_mcangle_it 1.153 r_mcbond_it 0.729 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.592 r_dihedral_angle_4_deg 23.135 r_dihedral_angle_3_deg 16.133 r_dihedral_angle_1_deg 5.371 r_scangle_it 2.948 r_scbond_it 1.826 r_angle_refined_deg 1.29 r_mcangle_it 1.153 r_mcbond_it 0.729 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5323 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing