2E8V | pdb_00002e8v

S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with product GGPP (P21)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DH4	PDB ENTRY 2DH4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.08M CH3COONa, 16% PEG 4000, 6-10% glycerol, 6-10% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.346	α = 90
b = 48.817	β = 111.59
c = 93.235	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0	NSRRC	BL13B1

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	1.8	30	98.8	0.051	28	4.37	64294	63682

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)
	1.8	1.86	97.1		0.522	2.73	3.9	6225

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DH4	1.8	24.7	64294	58217	2945	90.5	0.198	0.19	0.242	0.24	RANDOM	34.98

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	1.7
c_bond_d	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4724
Nucleic Acid Atoms
Solvent Atoms	980
Heterogen Atoms	58

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.