8JXK

Crystal Structure of Rv0047c from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	0.1M Sodium Acetate, 1.8M Sodium Formate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.17	α = 90
b = 102.17	β = 90
c = 191.88	γ = 120

Symmetry
Space Group	P 61

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++		2019-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	3.15	30.08	90.7	0.99	22.1	12.9		17786

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	3.15	3.37			0.94

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.15	30.076	17735	856	90.457	0.207	0.2042	0.2526	68.163

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]
24.963			24.963		-49.926

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.464
r_dihedral_angle_4_deg	20.429
r_dihedral_angle_3_deg	19.736
r_lrange_it	8.101
r_dihedral_angle_1_deg	5.835
r_scangle_it	4.642
r_mcangle_it	4.539
r_scbond_it	2.98
r_mcbond_it	2.829
r_angle_refined_deg	1.534
r_symmetry_xyhbond_nbd_refined	0.306
r_nbtor_refined	0.297
r_symmetry_nbd_refined	0.287
r_nbd_refined	0.239
r_ncsr_local_group_7	0.16
r_ncsr_local_group_1	0.159
r_ncsr_local_group_9	0.159
r_ncsr_local_group_8	0.155
r_ncsr_local_group_6	0.15
r_xyhbond_nbd_refined	0.149
r_ncsr_local_group_5	0.133
r_ncsr_local_group_10	0.129
r_ncsr_local_group_14	0.125
r_ncsr_local_group_12	0.123
r_ncsr_local_group_3	0.12
r_ncsr_local_group_2	0.118
r_ncsr_local_group_15	0.118
r_ncsr_local_group_13	0.116
r_chiral_restr	0.115
r_ncsr_local_group_11	0.115
r_ncsr_local_group_4	0.114
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6549
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms

Software

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