6PMU | pdb_00006pmu

Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VBE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.1 M Sodium malonate pH 6.0, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.387	α = 90
b = 91.387	β = 90
c = 137.426	γ = 90

Symmetry
Space Group	P 43 21 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 EIGER X 16M		2018-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	40	88.6	0.098	0.098	0.111	0.051	39	4.6		30969		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	99		0.428	0.428	0.476	0.202	0.88	3.7	5.4

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3vbe	2.1	40	29271	1488	88.61	0.1821	0.18	0.2234	RANDOM	35.336

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]
-1.27			-1.27		2.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.331
r_dihedral_angle_4_deg	20.331
r_dihedral_angle_3_deg	13.801
r_dihedral_angle_1_deg	6.333
r_angle_other_deg	2.347
r_angle_refined_deg	1.515
r_chiral_restr	0.079
r_bond_other_d	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.331
r_dihedral_angle_4_deg	20.331
r_dihedral_angle_3_deg	13.801
r_dihedral_angle_1_deg	6.333
r_angle_other_deg	2.347
r_angle_refined_deg	1.515
r_chiral_restr	0.079
r_bond_other_d	0.036
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4204
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.