2B8M | pdb_00002b8m

Crystal structure of a rmlc-like cupin family protein with a double-stranded beta-helix fold (mj0764) from methanocaldococcus jannaschii at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	277	0.2M (NH4)2SO4, 20.0% PEG-3350, No Buffer, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, pH 6

Crystal Properties
Matthews coefficient	Solvent content
1.91	39.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.83	α = 90
b = 49.83	β = 90
c = 78.74	γ = 120

Symmetry
Space Group	P 31 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		2005-09-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9796, 0.9797, 1.0000	ALS	8.2.2

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	1.7	29.08	99.3	0.091	7.84	3.48	12925	12267

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	1.7	1.76	97.2	97.2	0.527	2.23

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.7	29.08	12267	628	99.71	0.152	0.15197	0.149	0.16	0.204	0.21	RANDOM	20.146

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]
0.59	0.3		0.59		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.787
r_dihedral_angle_4_deg	24.987
r_dihedral_angle_3_deg	10.286
r_dihedral_angle_1_deg	7.208
r_scangle_it	6.923
r_scbond_it	5.057
r_mcangle_it	2.69
r_mcbond_it	2.307
r_angle_refined_deg	1.441
r_angle_other_deg	0.743
r_mcbond_other	0.582
r_nbd_refined	0.193
r_symmetry_vdw_other	0.189
r_nbd_other	0.18
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.174
r_symmetry_hbond_refined	0.155
r_symmetry_vdw_refined	0.093
r_chiral_restr	0.092
r_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	886
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing