2PGV | pdb_00002pgv

GTB C209A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LZ7	GTB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	6.8 mgml-1 GTB, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5 8 mM MnCl2, 2.5% (v/v) 2-methyl-2,4-pentanediol (MPD), 5% (v/v) glycerol, 2% (w/v) PEG 4000 and 0.3 0.5 mM 3-chloro-Hg-2-methoxy-propylurea suspended over a 1 ml reservoir solution (50 mM ADA, pH 7.5, 10 mM MnCl2, 100 mM ammonium sulfate, 5% (v/v) MPD, 10% (v/v) glycerol and 8 10% (w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.5	α = 90
b = 149.26	β = 90
c = 78.43	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV	Osmic	2006-05-23	M	SINGLE WAVELENGTH

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

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	1.79	19.76	93.5	0.049	13.3	3.99		27550

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	1.79	1.85	89.1		0.311	3.6	3.89

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	GTB	1.79	19.76	26134	1409	93.45	0.18731	0.18593	0.18	0.21254	0.21	RANDOM

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]
-0.86			-0.38		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.047
r_dihedral_angle_4_deg	18.026
r_dihedral_angle_3_deg	14.1
r_dihedral_angle_1_deg	6.204
r_scangle_it	3.532
r_scbond_it	2.258
r_mcangle_it	1.457
r_angle_refined_deg	1.437
r_mcbond_it	0.942
r_nbtor_refined	0.308
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.21
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.132
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2213
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	3

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
MOLREP	phasing