3GMI

Crystal structure of a protein of unknown function from Methanocaldococcus jannaschii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.2M Lithium chloride, 0.05M Magnesium sulfate, 8% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.935	α = 90
b = 73.988	β = 90
c = 85.024	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	SBC-2	Mirrors	2008-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9794	APS	19-BM

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	1.91	55.81	99.1	0.116	17.3	8.4	33730	33426		1.3

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	1.91	1.96	89.71		0.66	1.27	4.5	2546

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.91	55.81	33426	1768	99.1	0.1756	0.17388	0.20858	RANDOM	14.353

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]
0.3			-0.41		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.266
r_dihedral_angle_4_deg	17.702
r_dihedral_angle_3_deg	14.585
r_dihedral_angle_1_deg	5.512
r_scangle_it	5.126
r_scbond_it	3.157
r_mcangle_it	1.738
r_angle_refined_deg	1.643
r_angle_other_deg	0.92
r_mcbond_it	0.897

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.266
r_dihedral_angle_4_deg	17.702
r_dihedral_angle_3_deg	14.585
r_dihedral_angle_1_deg	5.512
r_scangle_it	5.126
r_scbond_it	3.157
r_mcangle_it	1.738
r_angle_refined_deg	1.643
r_angle_other_deg	0.92
r_mcbond_it	0.897
r_mcbond_other	0.282
r_chiral_restr	0.093
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2912
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	7

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SOLVE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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 R01GM133198.