4PVY | pdb_00004pvy

Crystal structure of human FPPS in complex with [({5-[4-(propan-2-yloxy)phenyl]pyridin-3-yl}amino)methanediyl]bis(phosphonic acid)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H5C	PDB ENTRY 4H5C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	295	1.7M sodium chloride, 15% glycerol, 0.085M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.06	α = 90
b = 111.06	β = 90
c = 67.03	γ = 90

Symmetry
Space Group	P 41 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	RIGAKU SATURN 944+	Rigaku Varimax-HF	2014-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	2.05	111.06	98.8	0.067	44.1	32.9	26578	26578			22.614

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	2.05	2.1	90.9		0.397	2.5	3	1769

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 4H5C	2.05	111.06	25246	25246	1288	98.7	0.1622	0.1622	0.15999	0.17	0.20573	0.22	RANDOM	32.252

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]
-1.98			-1.98		3.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.887
r_dihedral_angle_4_deg	21.795
r_dihedral_angle_3_deg	13.885
r_long_range_B_refined	6.581
r_long_range_B_other	6.58
r_dihedral_angle_1_deg	5.62
r_scangle_other	3.029
r_mcangle_it	2.013
r_mcangle_other	2.013
r_scbond_it	1.943
r_scbond_other	1.943
r_angle_refined_deg	1.786
r_mcbond_it	1.316
r_mcbond_other	1.314
r_angle_other_deg	0.919
r_chiral_restr	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2769
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	35

Software

Software
Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing