2YXE

Crystal structure of L-isoaspartyl protein carboxyl methyltranferase

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Oil batch	4.5	298	0.1M Acetate, 40% 1,2-propanediol, pH 4.5, Oil batch, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.267	α = 90
b = 84.448	β = 90
c = 123.091	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	RIGAKU JUPITER 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	98.1	0.037		6.9	43589	42769	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	84.5		0.24		4.9	3629

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JG4	2	20	40384	2143	98.52	0.1938	0.19182	0.23143	RANDOM	49.241

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]
2.94			1.48		-4.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.748
r_dihedral_angle_4_deg	16.581
r_dihedral_angle_3_deg	15.048
r_dihedral_angle_1_deg	6.464
r_scangle_it	4.785
r_scbond_it	3.078
r_mcangle_it	1.801
r_angle_refined_deg	1.8
r_mcbond_it	1.202
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.748
r_dihedral_angle_4_deg	16.581
r_dihedral_angle_3_deg	15.048
r_dihedral_angle_1_deg	6.464
r_scangle_it	4.785
r_scbond_it	3.078
r_mcangle_it	1.801
r_angle_refined_deg	1.8
r_mcbond_it	1.202
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.268
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3308
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.