2GNO | pdb_00002gno

Crystal structure of a dna polymerase iii, gamma subunit-related protein (tm0771) from thermotoga maritima msb8 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	6.2	277	35.0% 2-ethoxyethanol, 0.2M NaCl, 0.1M Na,K-Phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.56	α = 90
b = 135.56	β = 90
c = 35.56	γ = 90

Symmetry
Space Group	I 4

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	Flat mirror (vertical focusing)	2005-12-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979224, 0.918370, 0.978940	SSRL	BL11-1

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	27.9	94.7	0.041	11.88			22105			42.314

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	2.07	83.8		0.415	2

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	MAD	THROUGHOUT	2	27.94	22103	1130	99.26	0.223	0.22	0.23	0.278	0.28	RANDOM	34.573

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]
-0.96			-0.96		1.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.182
r_dihedral_angle_3_deg	8.319
r_dihedral_angle_4_deg	8.252
r_scangle_it	6.14
r_scbond_it	4.208
r_mcangle_it	2.42
r_dihedral_angle_1_deg	2.099
r_angle_refined_deg	1.684
r_mcbond_it	1.427
r_angle_other_deg	1.188
r_mcbond_other	0.385
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.18
r_xyhbond_nbd_refined	0.169
r_nbtor_refined	0.165
r_symmetry_vdw_refined	0.145
r_nbd_other	0.123
r_symmetry_vdw_other	0.109
r_chiral_restr	0.107
r_nbtor_other	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2346
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	17

Software

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