3QQV | pdb_00003qqv

Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5		0.15M POTASSIUM BROMIDE, PH 7.5, 30% PEG MME2000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.636	α = 90
b = 123.636	β = 90
c = 51.82	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	ADSC QUANTUM 315	MIRRORS	2010-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	40	99.9	0.1	7.1	12		30934		-5	41.976

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	2.03	100		0.9	10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	SAD	THROUGHOUT	2	40	29837	975	99.71	0.20911	0.20782	0.21	0.25213	0.2451	RANDOM	59.987

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]
2.16	1.08		2.16		-3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.197
r_dihedral_angle_4_deg	17.979
r_dihedral_angle_3_deg	14.711
r_scangle_it	9.609
r_scbond_it	6.344
r_mcangle_it	4.557
r_dihedral_angle_1_deg	4.525
r_mcbond_it	2.894
r_angle_refined_deg	1.141
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2710
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	48

Software

Software
Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing