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Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 0.1M tri-Sodium Citrate dihydrate pH 5.8, 24% PEG 4000, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.877 α = 90 b = 54.153 β = 90 c = 102.724 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 IMAGE PLATE RIGAKU RAXIS IV++ 2008-01-05 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 4r 2008-03-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97901, 0.97953, 0.96429 Photon Factory BL-6A
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 2.1 47.9 97.9 0.1 5.9 5.57 17458
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 2.1 2.18 98.8 0.334 2 5.82 1714
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 2.1 15 17384 896 97.85 0.187 0.183 0.1801 0.26 0.2493 RANDOM 23.175
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] -0.42 1.19 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.263 r_dihedral_angle_4_deg 16.643 r_dihedral_angle_3_deg 15.869 r_dihedral_angle_1_deg 6.307 r_scangle_it 3.776 r_scbond_it 2.656 r_mcangle_it 1.75 r_angle_refined_deg 1.723 r_mcbond_it 1.111 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.263 r_dihedral_angle_4_deg 16.643 r_dihedral_angle_3_deg 15.869 r_dihedral_angle_1_deg 6.307 r_scangle_it 3.776 r_scbond_it 2.656 r_mcangle_it 1.75 r_angle_refined_deg 1.723 r_mcbond_it 1.111 r_nbtor_refined 0.3 r_xyhbond_nbd_refined 0.29 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.204 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2084 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 6
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction SOLVE phasing