2Q80

Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		GGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	25% PEG 3350, 0.2M MG FORMATE, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.248	α = 90
b = 141.248	β = 90
c = 211.705	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	MARMOSAIC 225 mm CCD		2005-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.008	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	47.08	99.9	12	7.7	59513	59513

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.72	100		2.83	6.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	GGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)	2.7	47.08	57186	57186	2211	99.98	0.20434	0.20434	0.20246	0.25329	RANDOM	43.886

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.744
r_dihedral_angle_4_deg	18.695
r_dihedral_angle_3_deg	17.149
r_dihedral_angle_1_deg	5.521
r_scangle_it	1.855
r_angle_refined_deg	1.389
r_scbond_it	1.167
r_angle_other_deg	0.947
r_mcangle_it	0.735
r_mcbond_it	0.438
r_symmetry_vdw_other	0.286
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.232
r_nbtor_refined	0.191
r_nbd_other	0.178
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.161
r_metal_ion_refined	0.103
r_mcbond_other	0.094
r_nbtor_other	0.089
r_chiral_restr	0.07
r_xyhbond_nbd_other	0.055
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	13713
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	176

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling