8RP4

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (D156A mutant)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295.15	0.03 M magnesium chloride hexahydrate, 0.03 M calcium chloride dihydrate, 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000, 0.1 M sodium HEPES-MOPS,

Crystal Properties
Matthews coefficient	Solvent content
2.70480084	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.473	α = 90
b = 78.745	β = 92.151
c = 58.943	γ = 90

Symmetry
Space Group	C 1 2 1

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 XE 16M		2023-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.64	90.173	99	0.093	0.11	0.058	0.998	9.9	6.9		99692

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.67			2.09	2.456	1.283	0.372		7.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.64	90.173	99684	5055	98.828	0.18	0.1787	0.2108	27.835

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]
0.302		0.034	-0.718		0.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.053
r_dihedral_angle_3_deg	13.657
r_dihedral_angle_2_deg	12.36
r_lrange_it	6.778
r_lrange_other	6.759
r_dihedral_angle_1_deg	6.481
r_scangle_it	6.243
r_scangle_other	6.242
r_scbond_it	4.494
r_scbond_other	4.494
r_mcangle_it	4.181
r_mcangle_other	4.181
r_mcbond_other	3.379
r_mcbond_it	3.378
r_angle_refined_deg	2.113
r_angle_other_deg	0.759
r_nbd_other	0.328
r_symmetry_xyhbond_nbd_refined	0.244
r_nbd_refined	0.224
r_symmetry_nbd_refined	0.215
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.121
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5360
Nucleic Acid Atoms
Solvent Atoms	430
Heterogen Atoms	37

Software

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