8G8K | pdb_00008g8k

Crystal structure of Rv1916 (residues 233-398)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EDW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% (w/v) PEG3350, 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.046	α = 90
b = 86.046	β = 90
c = 73.586	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	85	PIXEL	DECTRIS EIGER X 16M		2018-08-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953724	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.54	46.89	100	0.999	12	26.6		41501

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.57	99.9		0.5

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 (All)	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	1.54	46.89	41435	2110	99.993	0.171	0.1702	0.18	0.19	0.2	RANDOM	27.503

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]
-0.534			-0.534		1.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.44
r_dihedral_angle_3_deg	12.632
r_lrange_it	7.637
r_lrange_other	7.625
r_scangle_it	6.718
r_scangle_other	6.715
r_dihedral_angle_2_deg	6.09
r_dihedral_angle_1_deg	5.946
r_scbond_it	4.531
r_scbond_other	4.528
r_mcangle_other	3.301
r_mcangle_it	3.299
r_mcbond_it	2.27
r_mcbond_other	2.27
r_angle_refined_deg	1.776
r_angle_other_deg	0.603
r_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.153
r_nbd_other	0.143
r_symmetry_nbd_refined	0.109
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1328
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	27

Software

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