2OGF

Crystal structure of protein MJ0408 from Methanococcus jannaschii, Pfam DUF372

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	24% PEG-3350, Tris-HCL, 0.2 M Ammonium Sulfate, pH 4.6, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.693	α = 90
b = 46.27	β = 118.54
c = 79.276	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2006-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.89	50	97.4	0.066	0.051	8.9	3.6	37996	37996

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	1.89	1.96	77.8		0.337	0.328	3	2.9	3018

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2IEC	1.89	27	37966	37966	1913	97.32	0.175	0.175	0.173	0.224	RANDOM	20.516

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]
-0.03		-0.11	-0.23		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.519
r_dihedral_angle_4_deg	16.872
r_dihedral_angle_3_deg	13.768
r_dihedral_angle_1_deg	5.726
r_scangle_it	3.049
r_scbond_it	2.073
r_angle_refined_deg	1.446
r_mcangle_it	1.081
r_mcbond_it	0.706
r_nbtor_refined	0.302
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.098
r_symmetry_hbond_refined	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3995
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	70

Software

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