7MFJ | pdb_00007mfj

Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PMU

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.801	α = 90
b = 91.801	β = 90
c = 140.122	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		2021-02-16	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)	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	2.35	40	99.1	0.098	0.098	0.127	0.037	0.941	17.5	11.5		25330

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	2.35	2.39	100		0.429	0.42	0.472	0.147	0.941	5	9.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6PMU	2.351	39.403	24758	1245	96.598	0.173	0.1708	0.18	0.2239	0.23	34.933

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]
-1.951			-1.951		3.901

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.529
r_dihedral_angle_4_deg	17.289
r_dihedral_angle_3_deg	13.378
r_lrange_it	6.517
r_lrange_other	6.489
r_dihedral_angle_1_deg	6.468
r_scangle_it	4.873
r_scangle_other	4.872
r_mcangle_it	3.891
r_mcangle_other	3.891
r_scbond_it	3.131
r_scbond_other	3.131
r_mcbond_it	2.595
r_mcbond_other	2.591
r_angle_refined_deg	1.433
r_angle_other_deg	1.306
r_nbd_other	0.253
r_nbd_refined	0.191
r_symmetry_nbd_other	0.182
r_symmetry_nbd_refined	0.18
r_symmetry_xyhbond_nbd_other	0.168
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.153
r_ncsr_local_group_1	0.084
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_refined	0.049
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4541
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	38

Software

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