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Crystal structure of the apo form of the E.coli ydhF protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PEG 4000 17.5%, IMIDAZOLE/MALATE 0.2M PH 7.0, AMMONIUM SULFATE 0.1M, GLYCEROL 2.5%, SPERMIDINE 0.1M
Crystal Properties Matthews coefficient Solvent content 2.05 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.722 α = 90 b = 87.722 β = 90 c = 66.168 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD MARRESEARCH MIRRORS 2002-03-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97917,0.98735,0.96 ESRF BM30A
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 2.57 16 98.7 0.078 6.3 5.4 9276 57.1
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 2.57 2.66 98.7 0.322 1.7 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.57 16.08 9239 969 99.3 0.2 0.2 0.1917 0.256 0.2491 RANDOM 38.6
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] -0.43 2.76 -0.43 0.87
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 2.74 c_mcangle_it 2.23 c_scbond_it 1.82 c_angle_deg 1.3 c_mcbond_it 1.29 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 2.74 c_mcangle_it 2.23 c_scbond_it 1.82 c_angle_deg 1.3 c_mcbond_it 1.29 c_improper_angle_d 0.8 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2362 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 5
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling autoSHARP phasing