1WMW | pdb_00001wmw

Crystal structure of geranulgeranyl diphosphate synthase from Thermus thermophilus

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	296	PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.88	α = 90
b = 139.88	β = 90
c = 73.35	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2000-02-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL40B2	0.97880, 0.97777, 0.97760, 0.96860	SPring-8	BL40B2

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	1.55	30	89.2	0.039		3.3	204955	182752	5.58	40.73	16.8

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	1.55	1.61	81.8		0.115

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	1.55	19.98	204846	182688	9157	89	0.175	0.175	0.18	0.198	0.2	RANDOM	18.1

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]
-0.87			-0.87		1.74

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18
c_scangle_it	3.22
c_scbond_it	2.33
c_mcangle_it	1.81
c_mcbond_it	1.3
c_angle_deg	1.2
c_improper_angle_d	0.9
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10139
Nucleic Acid Atoms
Solvent Atoms	1187
Heterogen Atoms

Software

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