3DKI | pdb_00003dki

2.1 A X-ray structure of CysM (Rv1336) from Mycobacterium tuberculosis an O-phosphoserine dependent cysteine synthase

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q3B	PDB ENTRY 2Q3B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.423	α = 90
b = 89.222	β = 90
c = 98.766	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	110	CCD	ADSC QUANTUM 315	Channel cut ESRF monochromator, Torodial focusing mirror	2008-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93400	ESRF	ID14-4

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	2.1	50	98.8	0.071	0.085	13.9	3.1	38897	38431		2.6	31.6

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)
1	2.1	2.21	99.7		0.453	0.539	2.6	3.2	5613

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2Q3B	2.1	28.58	2.6	37136	36490	1898	98.26	0.191	0.19343	0.19088	0.21	0.24147	0.25	RANDOM	23.102

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]
0.27			-1.1		0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.112
r_dihedral_angle_3_deg	15.845
r_dihedral_angle_4_deg	14.248
r_dihedral_angle_1_deg	5.851
r_scangle_it	3.236
r_scbond_it	2.029
r_angle_refined_deg	1.398
r_mcangle_it	1.275
r_angle_other_deg	0.957
r_mcbond_it	0.682
r_symmetry_hbond_refined	0.315
r_symmetry_vdw_other	0.28
r_symmetry_vdw_refined	0.268
r_nbd_refined	0.213
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.172
r_mcbond_other	0.138
r_nbtor_other	0.086
r_metal_ion_refined	0.086
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4567
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing