3FGP | pdb_00003fgp

2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis - Open and Closed Conformations

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DKI	PDB ENTRY 3DKI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	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
2.37	48.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.933	α = 90
b = 89.142	β = 90
c = 99.382	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	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	2.05	89.15	98.1	0.086	0.086	12.2	3.8	41528	41528	2	2	23.8

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)
	2.05	2.16	97		0.637	0.554	2	3.8	5922

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 (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 3DKI	2.05	50	41528	39379	2092	97.66	0.20041	0.19787	0.22	0.24671	0.26	RANDOM	23.818

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]
0.34			-0.55		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.815
r_dihedral_angle_3_deg	18.276
r_dihedral_angle_4_deg	16.958
r_dihedral_angle_1_deg	6.82
r_scangle_it	2.348
r_scbond_it	1.676
r_angle_refined_deg	1.484
r_mcangle_it	1.068
r_angle_other_deg	1.05
r_mcbond_it	0.914
r_symmetry_vdw_other	0.258
r_symmetry_hbond_refined	0.251
r_nbd_other	0.204
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.173
r_mcbond_other	0.143
r_chiral_restr	0.099
r_xyhbond_nbd_other	0.093
r_nbtor_other	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4801
Nucleic Acid Atoms
Solvent Atoms	324
Heterogen Atoms

Software

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