8RP3 | pdb_00008rp3

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis (H126A 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, HANGING 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
2.73654652	55.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.106	α = 90
b = 79.153	β = 91.656
c = 59.103	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		2022-11-24	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	2.45	90.52	100	0.368	0.434	0.228	0.982	4.9	6.9		30851

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	2.45	2.55			3.093	3.731	2.066	0.278		6.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	90.515	30847	1468	99.981	0.191	0.1875	0.2	0.2618	0.27	48.129

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]
0.136		0.69	-2.912		2.732

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.325
r_dihedral_angle_6_deg	15.107
r_lrange_other	11.586
r_lrange_it	11.585
r_dihedral_angle_2_deg	10.575
r_scangle_it	10.244
r_scangle_other	10.242
r_mcangle_other	9.516
r_mcangle_it	9.515
r_dihedral_angle_1_deg	7.955
r_scbond_it	7.828
r_scbond_other	7.826
r_mcbond_it	7.006
r_mcbond_other	6.994
r_angle_refined_deg	2.645
r_angle_other_deg	0.85
r_nbd_other	0.27
r_nbd_refined	0.239
r_symmetry_nbd_other	0.221
r_symmetry_nbd_refined	0.215
r_nbtor_refined	0.192
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.114
r_ncsr_local_group_1	0.114
r_symmetry_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5356
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	12

Software

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