3IWT | pdb_00003iwt

Structure of hypothetical molybdenum cofactor biosynthesis protein B from Sulfolobus tokodaii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y5E	PDB ENTRY 1y5e

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	7	298	10% W/V PEG 8000, 0.1M TRIS-HCL, 0.2M MGCL2, pH 7.0, MICROBATCH UNDER OIL, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.79	74.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.675	α = 90
b = 136.675	β = 90
c = 210.525	γ = 120

Symmetry
Space Group	P 64 2 2

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	MARMOSAIC 225 mm CCD	mirrors	2007-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.074	SRS	PX10.1

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	1.9	30	98.5	0.065		9	91510	91510			31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	97.7		0.61	0.5	2	4	8758

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1y5e	1.9	29.74	85236	89742	4506	98.16	0.16936	0.16936	0.16841	0.17	0.18695	0.19	RANDOM	47.856

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]
0.06	0.03		0.06		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.48
r_dihedral_angle_3_deg	12.912
r_dihedral_angle_4_deg	11.021
r_dihedral_angle_1_deg	5.622
r_scangle_it	2.865
r_scbond_it	2.195
r_angle_refined_deg	1.477
r_mcangle_it	1.234
r_mcbond_it	1.087
r_angle_other_deg	0.997
r_symmetry_vdw_refined	0.249
r_symmetry_vdw_other	0.225
r_nbd_refined	0.211
r_mcbond_other	0.205
r_symmetry_hbond_refined	0.197
r_nbd_other	0.191
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.172
r_metal_ion_refined	0.125
r_chiral_restr	0.093
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3882
Nucleic Acid Atoms
Solvent Atoms	581
Heterogen Atoms	70

Software

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