1XI8 | pdb_00001xi8

Molybdenum cofactor biosynthesis protein from Pyrococcus furiosus Pfu-1657500-001

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FC5	pdb entry 1FC5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch		291	25.5%w/v PEG-8000, 0.17M ammonium sulfate, 15%v/v glycerol, pH no buffer, modified microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.547	α = 90
b = 116.599	β = 90
c = 147.226	γ = 90

Symmetry
Space Group	P 21 21 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 210		2003-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	2.5	50	96.6	0.051				37143

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)
	2.5	2.59	81.2		0.316

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 (All)	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 1FC5	2.504	42.954	37001	1875	96.199	0.308	0.306	0.31	0.343	0.34	thin shells	52.75

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]
-0.018			0.038		-0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.751
r_dihedral_angle_3_deg	13.515
r_dihedral_angle_4_deg	13.271
r_dihedral_angle_1_deg	4.963
r_angle_refined_deg	1.267
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.318
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.176

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.751
r_dihedral_angle_3_deg	13.515
r_dihedral_angle_4_deg	13.271
r_dihedral_angle_1_deg	4.963
r_angle_refined_deg	1.267
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.318
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_mcbond_it
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4034
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.