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IspF (Burkholderia cenocepacia) 2CMP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0G PDB ENTRY 3F0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. BCISPF SAMPLE IN 100 MM NACL, 2MM MGCL2, 100 MM TRIS-HCL, PH 7.5; WAS CONCENTRATED TO 5 MG/ML, AND HAD CMP ADDED (20 MM CONCENTRATION IN SAMPLE). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITRES OF SAMPLE WITH 2 MICROLITRES RESERVOIR AT 20 DEGREES C. RESERVOIR SOLUTION: 25% W/V PEG 3350, 2.2M (NH4)2SO4, 0.1 M SODIUM FORMATE, PH 5.0, 1% V/V DIOXANE. CRYO: 20% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.849 α = 90 b = 89.316 β = 104.18 c = 72.981 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 IMAGE PLATE RIGAKU RAXIS IV PLUS PLUS 2011-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.9 19.32 99.9 0.14 6.2 3.4 47918 2 16.3
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 1.9 2 100 0.32 3.1 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3F0G 1.9 70.76 45493 2425 99.89 0.20601 0.20363 0.2079 0.25064 0.2533 RANDOM 17.204
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] 0.39 -0.67 0.53 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 17.138 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 5.352 r_angle_refined_deg 1.526 r_angle_other_deg 0.9 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.109 r_dihedral_angle_4_deg 17.138 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 5.352 r_angle_refined_deg 1.526 r_angle_other_deg 0.9 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3564 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing