9RZ2 | pdb_00009rz2

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-(4-(2-(3-Trifluoromethylphenethoxy)phenylthiol)propanoyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9I2T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.15	4 M ammonium acetate, 0.1 M Bis-Trispropane, pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 276.774	α = 90
b = 276.774	β = 90
c = 390.024	γ = 90

Symmetry
Space Group	I 4 2 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	PIXEL	DECTRIS EIGER2 X 16M		2024-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.953731	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.2	225.72	100	0.334	0.998	8.9	27.8		376404

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.24	100		0.396		27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.2	195.776	376356	18810	99.987	0.212	0.2096	0.2172	0.2488	0.253	45.807

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]
-0.112			-0.112		0.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.845
r_dihedral_angle_6_deg	15.08
r_dihedral_angle_2_deg	10.727
r_lrange_other	9.215
r_lrange_it	9.206
r_dihedral_angle_1_deg	7.133
r_mcangle_it	6.8
r_mcangle_other	6.8
r_scangle_it	6.777
r_scangle_other	6.776
r_mcbond_it	4.432
r_mcbond_other	4.432
r_scbond_it	4.39
r_scbond_other	4.39
r_angle_refined_deg	1.506
r_dihedral_angle_other_2_deg	1.387
r_angle_other_deg	0.48
r_nbd_refined	0.223
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_other	0.157
r_xyhbond_nbd_refined	0.155
r_nbd_other	0.143
r_symmetry_nbd_refined	0.122
r_symmetry_xyhbond_nbd_refined	0.087
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.067
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	32463
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms	864

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building