4AXK | pdb_00004axk

CRYSTAL STRUCTURE OF subHisA from the thermophile Corynebacterium efficiens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VEP	PDB ENTRY 2VEP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.1 M BIS-TRIS PH 7.5, 25% V/W PEG-3350, 0.2 M MGCL2,30% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.3	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.46	α = 90
b = 78.84	β = 90
c = 92.43	γ = 90

Symmetry
Space Group	P 21 21 21

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	MIRRORS	2009-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.25	56	99.4	0.09	16.2	7.1		24561		-3	48.3

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	2.25	2.37	96.1		1.12	2	6.6

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 2VEP	2.25	55.64	23607	957	99.42	0.23813	0.23556	0.23	0.30263	0.29	RANDOM	42.141

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]
1.13			-2.15		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.76
r_dihedral_angle_4_deg	21.967
r_dihedral_angle_3_deg	18.784
r_dihedral_angle_1_deg	7.001
r_scangle_it	3.652
r_scbond_it	2.204
r_mcangle_it	1.634
r_angle_refined_deg	1.606
r_mcbond_it	0.891
r_chiral_restr	0.12
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_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3626
Nucleic Acid Atoms
Solvent Atoms	83
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing