2CKD | pdb_00002ckd

Crystal structure of ML2640 from Mycobacterium leprae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PREVIOUS MODEL OBTAINED FROM SAD PHASING

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		1.6 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5, 50 MM MGCL2 (PROTEIN CONCENTRATION 11.8 MG/ML)

Crystal Properties
Matthews coefficient	Solvent content
2.9	56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.78	α = 90
b = 96.78	β = 90
c = 169.367	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM-210		2003-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.8	85	99.6	0.08	8	5.5		20669

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	2.8	2.95	99.9		0.25	3	5.6

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PREVIOUS MODEL OBTAINED FROM SAD PHASING	2.8	83.92	19338	1043	99.3	0.202	0.199	0.2	0.255	RANDOM	12.37

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]
-0.49			-0.49		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.973
r_dihedral_angle_3_deg	21.302
r_dihedral_angle_4_deg	20.382
r_dihedral_angle_1_deg	8.161
r_scangle_it	3.191
r_scbond_it	1.969
r_angle_refined_deg	1.826
r_mcangle_it	1.293
r_mcbond_it	0.765
r_nbtor_refined	0.327
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.198
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.124
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
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_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	4692
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing