2QIS

Crystal structure of human farnesyl pyrophosphate synthase T210S mutant bound to risedronate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZW5PDB entry 1ZW5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72980.20 M NH4Cl, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.47α = 90
b = 111.47β = 90
c = 67.603γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.97956SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.84299.40.06314.94.8397443974430
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.91000.5662.44.75754

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1ZW51.830.923771037710199699.230.179260.179260.17780.20593RANDOM34.418
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]
-1.43-1.432.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.582
r_dihedral_angle_4_deg17.817
r_dihedral_angle_3_deg13.585
r_scangle_it6.626
r_scbond_it5.025
r_dihedral_angle_1_deg4.672
r_mcangle_it2.947
r_mcbond_it2.175
r_angle_refined_deg1.255
r_angle_other_deg0.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.582
r_dihedral_angle_4_deg17.817
r_dihedral_angle_3_deg13.585
r_scangle_it6.626
r_scbond_it5.025
r_dihedral_angle_1_deg4.672
r_mcangle_it2.947
r_mcbond_it2.175
r_angle_refined_deg1.255
r_angle_other_deg0.911
r_mcbond_other0.593
r_nbd_refined0.217
r_symmetry_vdw_other0.194
r_nbtor_refined0.187
r_nbd_other0.174
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.097
r_nbtor_other0.086
r_chiral_restr0.07
r_metal_ion_refined0.019
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2672
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing