4CKZ | pdb_00004ckz

Structure of the Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y71	PDB ENTRY 2Y71

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.4		32% PEG 4000, 0.1 M NA CITRATE PH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.42	α = 90
b = 38.42	β = 90
c = 132	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)	2013-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC		ALBA	XALOC

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	2.51	44	80.7	0.16	13.3	8.2		6028		-3	51.8

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	2.51	2.65	20.4		0.44	6.4	8

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 2Y71	2.52	44	5752	272	81.48	0.24169	0.23734	0.24	0.33557	0.35	RANDOM	33.032

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]
-0.07			-0.07		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.569
r_dihedral_angle_3_deg	17.473
r_dihedral_angle_4_deg	12.118
r_dihedral_angle_1_deg	6.614
r_scbond_it	4.7
r_mcangle_it	1.675
r_angle_refined_deg	1.081
r_mcbond_it	0.935
r_scangle_it	0.72
r_angle_other_deg	0.684
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.198
r_nbd_other	0.167
r_nbtor_refined	0.164
r_symmetry_vdw_other	0.154
r_symmetry_hbond_refined	0.149
r_mcbond_other	0.135
r_nbtor_other	0.082
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	1916
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing