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CRYSTAL STRUCTURE OF FARNESYL DIPHOSPHATE SYNTHASE (TARGET EFI-501951) FROM Methylococcus capsulatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P41 PDB ENTRY 3P41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 294 0.1M TRIS-HCL, 2M AMMONIUM PHOSPHATE MONOBASIC, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.592 α = 90 b = 114.592 β = 90 c = 113.19 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 MIRRORS 2011-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.94 50 94 0.131 7 15.3 56269 -5 37.836
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 1.94 1.97 96.6 0.95 1.1 14.1
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 3P41 1.94 50 51174 1631 93.85 0.2206 0.21915 0.2186 0.26577 0.2654 RANDOM 47.28
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] 0.33 0.33 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.565 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_4_deg 15.396 r_scangle_it 11.027 r_scbond_it 7.967 r_mcangle_it 5.181 r_dihedral_angle_1_deg 4.626 r_mcbond_it 3.734 r_angle_refined_deg 1.292 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.565 r_dihedral_angle_3_deg 16.839 r_dihedral_angle_4_deg 15.396 r_scangle_it 11.027 r_scbond_it 7.967 r_mcangle_it 5.181 r_dihedral_angle_1_deg 4.626 r_mcbond_it 3.734 r_angle_refined_deg 1.292 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4462 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 25
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling