3D2O

Crystal Structure of Manganese-metallated GTP Cyclohydrolase Type IB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	(PEG 6000, 10-16%), LiCl (1-1.4 M), Tris (50 mM, pH 9.0) and Tris-Cl (50 mM, pH 7.0). Enzym sample prepared at 10 mg/mL in 50 mM Tris-HCl, 50 mM KCl, 1 mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.225	α = 90
b = 100.42	β = 90
c = 113.947	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315		2008-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97607	SSRL	BL7-1

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	2.04	50	99.8	0.071	11	4.5	33675	33675

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	2.04	2.11	99.9		0.428		4.5	3314

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3D1T	2.04	30.33	33647	1710	99.66	0.189	0.185	0.264	RANDOM	37.382

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]
-0.09			0.02		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.185
r_dihedral_angle_4_deg	22.331
r_dihedral_angle_3_deg	16.604
r_sphericity_free	8.842
r_dihedral_angle_1_deg	6.962
r_scangle_it	4.451
r_sphericity_bonded	4.391
r_scbond_it	3.29
r_rigid_bond_restr	2.302
r_mcangle_it	2.184
r_angle_refined_deg	1.754
r_mcbond_it	1.42
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.24
r_nbd_refined	0.22
r_metal_ion_refined	0.181
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3829
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing