3Q2Q

Crystal structure of geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum complexed with calcium and isoprenyl diphosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5		0.1M SODIUM ACETATE, PH 4.5, 30% PEG400, 200MM CALCIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.659	α = 90
b = 71.659	β = 90
c = 150.919	γ = 120

Symmetry
Space Group	P 32 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	2010-02-25	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	1.9	40	99.8	0.075	10.1	6.4		36231		-5	37.374

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	1.9	1.93	100		0.9	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	3LMD	1.9	40	34942	1118	99.68	0.18428	0.18317	0.21761	RANDOM	51.085

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	0.99		1.98		-2.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.565
r_dihedral_angle_4_deg	14.816
r_dihedral_angle_3_deg	14.66
r_scangle_it	10.196
r_scbond_it	6.922
r_mcangle_it	5.098
r_dihedral_angle_1_deg	3.928
r_mcbond_it	3.521
r_angle_refined_deg	1.03
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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	2398
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	29

Software

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