9I2W | pdb_00009i2w

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with flurbiprofenoyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8RMW

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
4.06	69.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 276.476	α = 90
b = 276.476	β = 90
c = 391.895	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		2024-04-25	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)	Rpim I (All)	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	225.914	100	0.407	0.079	0.994	7.1	27.3		377344

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	12.05	225.91	99.8		0.058	0.012	0.99	21.1	25.2

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	225.914	377256	19315	99.976	0.212	0.2106	0.2197	0.2453	0.2531	46.445

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]
0.057			0.057		-0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.018
r_dihedral_angle_3_deg	15.916
r_dihedral_angle_6_deg	14.494
r_lrange_other	9.794
r_lrange_it	9.782
r_dihedral_angle_1_deg	7.244
r_scangle_it	7.212
r_scangle_other	7.212
r_mcangle_it	7.112
r_mcangle_other	7.112
r_scbond_it	4.664
r_scbond_other	4.664
r_mcbond_it	4.638
r_mcbond_other	4.638
r_dihedral_angle_other_2_deg	2.623
r_angle_refined_deg	1.806
r_angle_other_deg	0.592
r_nbd_refined	0.225
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.182
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.113
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.081
r_symmetry_nbd_refined	0.081
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.008
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	32491
Nucleic Acid Atoms
Solvent Atoms	1167
Heterogen Atoms	780

Software

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