9CY2 | pdb_00009cy2

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, JDS05120


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5295.150.085 M HEPES (pH 7.5), 17% (w/v) PEG 10000, 6.8% (v/v) ethylene glycol, 15% (v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.95α = 90
b = 110.95β = 90
c = 73.9γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.249.6298.90.0410.0450.01524.78.92366259.516
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2697.21.0041.1260.3742.28.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.249.61823638119798.5410.1910.18820.21160.24620.2648Random81.006
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]
-5.027-5.02710.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.044
r_dihedral_angle_3_deg14.331
r_dihedral_angle_2_deg11.39
r_lrange_other9.385
r_lrange_it9.381
r_scangle_it6.592
r_scangle_other6.59
r_dihedral_angle_1_deg6.031
r_mcangle_it4.771
r_mcangle_other4.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.044
r_dihedral_angle_3_deg14.331
r_dihedral_angle_2_deg11.39
r_lrange_other9.385
r_lrange_it9.381
r_scangle_it6.592
r_scangle_other6.59
r_dihedral_angle_1_deg6.031
r_mcangle_it4.771
r_mcangle_other4.77
r_scbond_other4.394
r_scbond_it4.393
r_mcbond_it3.298
r_mcbond_other3.295
r_angle_refined_deg1.435
r_angle_other_deg0.502
r_nbd_refined0.231
r_xyhbond_nbd_refined0.197
r_nbtor_refined0.193
r_symmetry_nbd_other0.189
r_nbd_other0.151
r_symmetry_nbtor_other0.072
r_chiral_restr0.068
r_symmetry_xyhbond_nbd_refined0.062
r_symmetry_nbd_refined0.035
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2674
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing