3BRC | pdb_00003brc

Crystal structure of a conserved protein of unknown function from Methanobacterium thermoautotrophicum

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.1M Ammonium phosphate, 16% PEG 3350, 2% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.894	α = 90
b = 48.916	β = 118.54
c = 63.868	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315	Mirrors	2007-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97940	APS	19-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	1.6	88.52	88.52	0.09	27.05	4.4	36473	32286		2	18

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	1.6	1.642	40.92		0.378	1.35	2	2852

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.6	56.08	32286	32286	1703	88.52	0.18586	0.18586	0.18324	0.2004	0.23669	0.2453	RANDOM	17.697

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]
1.64		1.07	-0.95		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.668
r_dihedral_angle_4_deg	20.762
r_dihedral_angle_3_deg	14.154
r_dihedral_angle_1_deg	5.053
r_scangle_it	4.73
r_scbond_it	3.582
r_mcbond_it	1.949
r_mcangle_it	1.932
r_angle_refined_deg	1.312
r_angle_other_deg	0.924
r_mcbond_other	0.55
r_symmetry_vdw_other	0.288
r_nbd_refined	0.246
r_nbd_other	0.22
r_symmetry_vdw_refined	0.218
r_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.132
r_nbtor_other	0.083
r_chiral_restr	0.075
r_bond_refined_d	0.013
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	2437
Nucleic Acid Atoms
Solvent Atoms	226
Heterogen Atoms	15

Software

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