5YDD

Crystal structure of C-terminal domain of Rv1828 from Mycobacterium tuberculosis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	2.2 M Ammonium sulfate, 0.1 M Bis-Tris (pH 6.5)

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.035	α = 90
b = 31.452	β = 97.76
c = 76.998	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2016-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97625	ESRF	BM14

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	1.5	50	96.2	0.02	23.3	2.7		33255		-3	15.6

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	1.5	1.53	93.6		0.46	1.6	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5YDC	1.5	27.24	31581	1671	96.1	0.157	0.154	0.209	RANDOM	21.1

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		-1.53	-1.78		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.371
r_dihedral_angle_2_deg	35.065
r_sphericity_bonded	17.149
r_dihedral_angle_4_deg	13.747
r_dihedral_angle_3_deg	12.703
r_long_range_B_refined	4.945
r_long_range_B_other	4.944
r_dihedral_angle_1_deg	4.445
r_scangle_other	3.573
r_scbond_it	3.157
r_scbond_other	3.153
r_mcangle_it	2.696
r_mcangle_other	2.695
r_rigid_bond_restr	2.308
r_mcbond_it	2.211
r_mcbond_other	2.147
r_angle_refined_deg	1.608
r_angle_other_deg	1.014
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1780
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing