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Crystal structure of putative transcriptional regulator ycdc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 290 SODIUM CHLORIDE, SODIUM FORMATE, GLYCEROL, PH 7, VAPOR DIFFUSION, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 3.15 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.02 α = 90 b = 139.61 β = 90 c = 156 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 200 CCD SBC-3 MIRRORS 2003-03-11 M SINGLE WAVELENGTH 2 1 x-ray 200 IMAGE PLATE MARRESEARCH MIRRORS 2003-03-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.96367 APS 19-BM 2 SYNCHROTRON NSLS BEAMLINE X9A 0.972, 0.9786, 0.9789 NSLS X9A
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 2.5 50 99.8 0.064 0.093 8 4.48 40218 40218
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) 2.5 2.59 99.3 0.44 0.43 2.1 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.5 49.35 36793 36793 1931 96.21 0.19704 0.19704 0.19537 0.2113 0.22905 RANDOM 14.4
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] 0.88 -2.28 1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_1_deg 5.267 r_scangle_it 3.132 r_angle_other_deg 2.243 r_scbond_it 2.123 r_angle_refined_deg 1.447 r_mcangle_it 0.944 r_mcbond_it 0.485
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 19.198 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_1_deg 5.267 r_scangle_it 3.132 r_angle_other_deg 2.243 r_scbond_it 2.123 r_angle_refined_deg 1.447 r_mcangle_it 0.944 r_mcbond_it 0.485 r_chiral_restr 0.084 r_mcbond_other 0.08 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6235 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 32
Software Software Software Name Purpose SBC-Collect data collection SOLVE phasing RESOLVE model building HKL-3000 phasing REFMAC refinement Coot model building DENZO data reduction SCALEPACK data scaling RESOLVE phasing