3N4G | pdb_00003n4g

Crystal structure of native Cg10062

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N4D	PDB ENTRY 3N4D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4	298	6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), Hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.097	α = 90
b = 40.69	β = 94.96
c = 89.938	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	IMAGE PLATE	RIGAKU RAXIS IV		2005-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.43	50	99	0.059	23.5	3		14190

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	2.43	2.52	99.1		0.17		2.9	1396

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3N4D	2.44	25	14187	712	98.85	0.211	0.209	0.23	0.259	0.24	RANDOM	33.669

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.607
r_dihedral_angle_3_deg	18.608
r_dihedral_angle_4_deg	15.376
r_dihedral_angle_1_deg	5.158
r_angle_refined_deg	1.799
r_scangle_it	0.973
r_mcangle_it	0.759
r_scbond_it	0.578
r_mcbond_it	0.424
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.205
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.07
r_bond_refined_d	0.021
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3522
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms

Software

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