2QV6 | pdb_00002qv6

GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	17% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.203	α = 90
b = 129.578	β = 90
c = 90.876	γ = 90

Symmetry
Space Group	P 21 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	295	IMAGE PLATE	RIGAKU RAXIS IV++	confocal blue	2007-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2	31.3	94.6	0.083	8.7	3.9		76172			25.7

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)
	2	2.07	92.7		0.422	2.9	3.6	7350

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	MAD	THROUGHOUT	2	31.31	72282	3845	94.57	0.20829	0.20632	0.2085	0.24431	0.2431	RANDOM	26.675

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]
-0.66			2.11		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.075
r_dihedral_angle_4_deg	23.942
r_dihedral_angle_3_deg	16.032
r_dihedral_angle_1_deg	5.954
r_scangle_it	3.245
r_scbond_it	2.063
r_angle_refined_deg	1.523
r_mcangle_it	1.247
r_angle_other_deg	0.979
r_mcbond_it	0.666
r_nbd_refined	0.232
r_symmetry_vdw_other	0.212
r_nbd_other	0.196
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.156
r_metal_ion_refined	0.151
r_mcbond_other	0.14
r_symmetry_hbond_refined	0.088
r_chiral_restr	0.086
r_nbtor_other	0.086
r_symmetry_vdw_refined	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
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	8049
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	140

Software

Software
Software Name	Purpose
CrystalClear	data collection
SOLVE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling