1VJK | pdb_00001vjk

Putative molybdopterin converting factor, subunit 1 from Pyrococcus furiosus, Pfu-562899-001

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	modified microbatch	6.5	291	100mM sodium cacodylate, 30% PEG 8000, 200mM ammonium sulfate, modified microbatch, temperature 291K, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.467	α = 90
b = 81.467	β = 90
c = 63.698	γ = 120

Symmetry
Space Group	P 65 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				SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97	APS	22-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	1.51	50	99.3	0.065				19993

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	1.51	1.56	100		0.16

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.51	70.711	18936	1021	99.24	0.211	0.21	0.23	0.2243	0.25	RANDOM	13.587

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]
0.225	0.112		0.225		-0.337

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.951
r_scangle_it	4.431
r_mcangle_it	2.834
r_scbond_it	2.817
r_mcbond_it	1.863
r_angle_refined_deg	1.322
r_nbtor_refined	0.311
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.135
r_symmetry_hbond_refined	0.104

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.951
r_scangle_it	4.431
r_mcangle_it	2.834
r_scbond_it	2.817
r_mcbond_it	1.863
r_angle_refined_deg	1.322
r_nbtor_refined	0.311
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.135
r_symmetry_hbond_refined	0.104
r_chiral_restr	0.09
r_xyhbond_nbd_refined	0.075
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	702
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ARP/wARP	model building
XFIT	data reduction
MolProbity	model building

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.