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crystal structure of hypothetical dTDP-4-dehydrorhamnose reductase from sulfolobus tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N2S PDB ENTRY 1N2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 14% PEG 3350, 0.1M KI, 20% BENZAMIDINE, 20mM TRIS-HCL, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.944 α = 90 b = 40.683 β = 116.18 c = 103.14 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 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 1.7 50 98.9 63625 62990
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 92.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1N2S 1.7 19.87 62990 59772 3203 98.99 0.21009 0.20782 0.2061 0.2531 0.2529 RANDOM 27.449
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] -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_3_deg 15.681 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 10.511 r_scangle_it 3.696 r_scbond_it 2.532 r_angle_refined_deg 1.716 r_mcangle_it 1.578 r_mcbond_it 0.981 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.105 r_dihedral_angle_3_deg 15.681 r_dihedral_angle_4_deg 14.188 r_dihedral_angle_1_deg 10.511 r_scangle_it 3.696 r_scbond_it 2.532 r_angle_refined_deg 1.716 r_mcangle_it 1.578 r_mcbond_it 0.981 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.279 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.146 r_symmetry_hbond_refined 0.143 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4369 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALEPACK data scaling MOLREP phasing