4JVJ | pdb_00004jvj

Crystal structure of human FPPS in complex with magnesium, CL01131, and sulfate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.15	8% PEG8000, 0.1 M TRIS, 0.2 M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.33	α = 90
b = 111.33	β = 90
c = 67.462	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	RAYONIX MX-300		2013-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

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	2.8	50	98.6	0.073	27.3	9.5	10724	10724

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	2.8	2.85	99.6		0.26	6.6	9.6	503

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 4DEM	2.8	49.84	10170	10170	509	98.04	0.23845	0.23845	0.23584	0.2371	0.28828	0.302	RANDOM	63.717

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]
-7.57			-7.57		15.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.995
r_dihedral_angle_3_deg	17.505
r_dihedral_angle_4_deg	13.095
r_dihedral_angle_1_deg	6.683
r_angle_refined_deg	1.434
r_angle_other_deg	0.818
r_chiral_restr	0.069
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2648
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	34

Software

Software
Software Name	Purpose
MxDC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing