3RNS | pdb_00003rns

Cupin 2 conserved barrel domain protein from Leptotrichia buccalis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	0.1 M Bis-Tris-Propane:NaOH, 1.8 M sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.684	α = 90
b = 58.684	β = 90
c = 143.542	γ = 90

Symmetry
Space Group	P 41 21 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	ADSC QUANTUM 315r		2011-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	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	2.07	35.9	99.9	0.103	9	13	16116	16116			46.6

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)
	2.07	2.11	100		0.892	2.77	10.9	792

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.07	35.9	15938	15938	785	99.03	0.1734	0.1734	0.1717	0.2081	0.1998	RANDOM	43.4159

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]
1.35			1.35		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.74
r_dihedral_angle_3_deg	16.262
r_dihedral_angle_4_deg	12.425
r_dihedral_angle_1_deg	6.603
r_scangle_it	4.585
r_scbond_it	2.819
r_mcangle_it	1.827
r_angle_refined_deg	1.701
r_mcbond_it	0.999
r_angle_other_deg	0.887
r_mcbond_other	0.256
r_chiral_restr	0.107
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	1633
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing