9I2Z | pdb_00009i2z

Alpha-Methylacyl-CoA racemase from Mycobacterium tuberculosis in complex with 2-methyldecanoyl-CoA

X-RAY DIFFRACTION

---

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
4.04	69.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 277.034	α = 90
b = 277.034	β = 90
c = 390.861	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	2.11	226.02	100	0.267	0.052	0.996	10	27.4		427911

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	11.56	226.02	99.9		0.046	0.009	0.993	34.9	25.6

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	2.11	226.019	427679	21361	99.945	0.203	0.201	0.2078	0.239	0.2464	45.194

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]
0.009			0.009		-0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.33
r_dihedral_angle_6_deg	14.383
r_dihedral_angle_2_deg	8.571
r_lrange_other	8.485
r_lrange_it	8.483
r_dihedral_angle_1_deg	7.165
r_scangle_it	6.601
r_scangle_other	6.6
r_mcangle_other	6.382
r_mcangle_it	6.381
r_scbond_other	4.403
r_scbond_it	4.402
r_mcbond_it	4.341
r_mcbond_other	4.341
r_dihedral_angle_other_2_deg	3.151
r_angle_refined_deg	1.838
r_angle_other_deg	0.596
r_nbd_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.197
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.134
r_nbd_other	0.127
r_symmetry_xyhbond_nbd_other	0.124
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.068
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	32536
Nucleic Acid Atoms
Solvent Atoms	1668
Heterogen Atoms	720

Software

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