3D0Q | pdb_00003d0q

Crystal structure of calG3 from Micromonospora echinospora determined in space group I222

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (16% PEG 4000, 0.20 M Tri-ammonium citrate, 0.10 M MOPS pH 7.0). Cryoprotected in well solution containing up to 20% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.654	α = 90
b = 119.267	β = 90
c = 155.942	γ = 90

Symmetry
Space Group	I 2 2 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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97918	APS	23-ID-D

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	2.79	27	99.2	0.121	9.819	7.3		24883

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	2.79	2.9	94.9		0.426	4.046	6.3	2342

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.79	26.75	24883	1270	98.883	0.19	0.187	0.1926	0.243	0.236	RANDOM	11.99

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]
5.326			-2.249		-3.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.542
r_dihedral_angle_4_deg	19.492
r_dihedral_angle_3_deg	17.304
r_scangle_it	8.431
r_dihedral_angle_1_deg	5.578
r_scbond_it	5.453
r_mcangle_it	2.7
r_mcbond_it	1.44
r_angle_refined_deg	1.337
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.542
r_dihedral_angle_4_deg	19.492
r_dihedral_angle_3_deg	17.304
r_scangle_it	8.431
r_dihedral_angle_1_deg	5.578
r_scbond_it	5.453
r_mcangle_it	2.7
r_mcbond_it	1.44
r_angle_refined_deg	1.337
r_nbtor_refined	0.314
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.13
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5716
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	26

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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 R01GM157729.