3H7F

Crystal structure of serine hydroxymethyltransferase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DKJ	pdb entry 2dkj modified by ccp4 program chainsaw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	HAMPTON INDEX, G12: 25% PEG 3350, 200MM MGCL2, 100MM HEPES, MYTUD.00783.A AT 20 MG/ML, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.73	α = 90
b = 102.01	β = 90
c = 132.12	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 315r	Single crystal, cylindrically bent, Si(220)	2009-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

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	80.74	99.3	0.06	13.55	5	130938	130938		-3	24.67

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	1.54	98.9		0.463	2.4	3.5	9515

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 2dkj modified by ccp4 program chainsaw	1.5	20	130877	130877	6606	99.3	0.166	0.166	0.165	0.196	RANDOM	16.21

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]
-0.06			-1.12		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.072
r_dihedral_angle_4_deg	15.58
r_dihedral_angle_3_deg	12.112
r_dihedral_angle_1_deg	5.965
r_scangle_it	3.421
r_scbond_it	2.177
r_angle_refined_deg	1.629
r_mcangle_it	1.334
r_angle_other_deg	1.168
r_mcbond_it	0.803
r_mcbond_other	0.245
r_chiral_restr	0.101
r_bond_refined_d	0.023
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6238
Nucleic Acid Atoms
Solvent Atoms	962
Heterogen Atoms	1

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling