4PVX | pdb_00004pvx

Crystal structure of human FPPS in complex with [({4-[4-(cyclopropyloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4H5CPDB ENTRY 4H5C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62955.6% PEG 4000, 30% glycerol, 0.07M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.26α = 90
b = 111.26β = 90
c = 69.34γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+Rigaku Varimax-HF2014-01-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.1869.3498.60.06253.819.7229812298128.4
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)
12.182.2498.90.6533.510.91671

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 4H5C2.1869.342177421774116798.580.172290.172290.169740.180.220080.23RANDOM38.974
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]
-2.82-2.825.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.289
r_dihedral_angle_4_deg18.67
r_dihedral_angle_3_deg15.101
r_dihedral_angle_1_deg5.621
r_long_range_B_refined5.438
r_long_range_B_other5.438
r_scangle_other3.515
r_mcangle_it2.321
r_mcangle_other2.32
r_scbond_it2.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.289
r_dihedral_angle_4_deg18.67
r_dihedral_angle_3_deg15.101
r_dihedral_angle_1_deg5.621
r_long_range_B_refined5.438
r_long_range_B_other5.438
r_scangle_other3.515
r_mcangle_it2.321
r_mcangle_other2.32
r_scbond_it2.287
r_scbond_other2.286
r_angle_refined_deg1.707
r_mcbond_it1.612
r_mcbond_other1.61
r_angle_other_deg0.909
r_chiral_restr0.095
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2751
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms35

Software

Software
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing