8RP5 | pdb_00008rp5

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (E241A mutant)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X74

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, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.71437407	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.619	α = 90
b = 78.989	β = 92.191
c = 58.923	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 X 16M		2022-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

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	1.85	90.244	100	0.128	0.152	0.081	0.998	8.2	6.8		70688

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	1.85	1.89			1.823	2.156	1.142	0.5		6.9

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	1.85	90.244	70667	3590	99.967	0.195	0.193	0.2	0.2363	0.24	31.274

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]
0.083		0.418	-2.186		2.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.034
r_dihedral_angle_3_deg	14.779
r_dihedral_angle_2_deg	8.764
r_lrange_it	8.013
r_lrange_other	7.994
r_dihedral_angle_1_deg	7.207
r_scangle_it	6.86
r_scangle_other	6.859
r_mcangle_it	5.385
r_mcangle_other	5.385
r_scbond_it	5.012
r_scbond_other	5.011
r_mcbond_it	4.152
r_mcbond_other	4.152
r_angle_refined_deg	2.323
r_angle_other_deg	0.803
r_nbd_other	0.261
r_nbd_refined	0.244
r_symmetry_xyhbond_nbd_refined	0.222
r_symmetry_nbd_other	0.211
r_nbtor_refined	0.189
r_symmetry_nbd_refined	0.186
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_other	0.132
r_chiral_restr	0.118
r_symmetry_nbtor_other	0.091
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	5358
Nucleic Acid Atoms
Solvent Atoms	414
Heterogen Atoms	34

Software

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