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IspH in complex with propynyl diphosphate (1061)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KE8 PDB ENTRY 3KE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M BIS-TRIS, 0.2 M ammonia sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.63 α = 90 b = 80.57 β = 90 c = 111.86 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 PIXEL PSI PILATUS 6M 2010-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.5 47.98 99 0.059 13.7 103709 102672 2 2
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 1.5 1.6 97.6 0.429 4.2
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 3KE8 1.5 47.98 101224 96162 5062 100 0.16368 0.16121 0.1711 0.21154 0.2195 RANDOM 17.619
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] 0.35 -1.14 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.1 r_dihedral_angle_4_deg 21.373 r_dihedral_angle_3_deg 15.472 r_sphericity_free 10.776 r_scangle_it 6.949 r_sphericity_bonded 5.882 r_dihedral_angle_1_deg 5.57 r_scbond_it 4.852 r_mcangle_it 3.35 r_rigid_bond_restr 2.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.1 r_dihedral_angle_4_deg 21.373 r_dihedral_angle_3_deg 15.472 r_sphericity_free 10.776 r_scangle_it 6.949 r_sphericity_bonded 5.882 r_dihedral_angle_1_deg 5.57 r_scbond_it 4.852 r_mcangle_it 3.35 r_rigid_bond_restr 2.959 r_mcbond_it 2.393 r_angle_refined_deg 2.323 r_chiral_restr 0.255 r_bond_refined_d 0.026 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4773 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 40
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing