3DK5 | pdb_00003dk5

Crystal Structure of Apo-GlmU from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	8% PEG 8000, 150mM NaCl, 2mM MnCl2, 5%Glycerol, 1,3-butanediol, AMPPNP, MgCl2, DTT, pH 7.5, vapor diffusion, sitting drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.6	α = 90
b = 79.6	β = 90
c = 278	γ = 120

Symmetry
Space Group	H 3

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	MAR scanner 345 mm plate	mirrors	2008-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54179

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	2.23	30	98.2	0.123	11.3			31336		-3	42.935

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)
	2.23	2.29	80.9		0.723	2.4

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 (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	2.23	29.3	31334	1567	100	0.227	0.225	0.2415	0.271	0.2802	RANDOM	43.241

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]
1.78	0.89		1.78		-2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.841
r_dihedral_angle_4_deg	22.998
r_dihedral_angle_3_deg	15.631
r_dihedral_angle_1_deg	8.205
r_scangle_it	6.119
r_scbond_it	4.091
r_mcangle_it	2.425
r_angle_refined_deg	2.26
r_mcbond_it	1.534
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.273
r_nbd_refined	0.232
r_chiral_restr	0.157
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.137
r_bond_refined_d	0.028
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3144
Nucleic Acid Atoms
Solvent Atoms	102
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection