2ZYQ

Crystal structure of the HsaC extradiol dioxygenase from M. tuberculosis

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KND	PDB ENTRY 1KND

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	298	pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.737	α = 90
b = 123.737	β = 90
c = 106.784	γ = 90

Symmetry
Space Group	P 4 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	100	IMAGE PLATE	MAR scanner 345 mm plate		2006-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.541

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	26	99.9	0.094	0.091	7.7	14	56597	56445		1	21.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.2	99.9		0.458	0.441	1.6	13.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1KND	2	20	53592	53536	2861	100	0.18	0.182	0.18	0.223	RANDOM	19.41

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]
-0.53			-0.53		1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.827
r_dihedral_angle_4_deg	17.957
r_dihedral_angle_3_deg	16.146
r_dihedral_angle_1_deg	10.497
r_angle_refined_deg	1.673
r_mcangle_it	1.344
r_mcbond_it	0.893
r_nbtor_refined	0.298
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.169
r_chiral_restr	0.132
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4677
Nucleic Acid Atoms
Solvent Atoms	675
Heterogen Atoms	12

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling