8B9W | pdb_00008b9w

Cysteine Synthase from Trypanosoma theileri with PLP bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AIR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Ammonium sulfate, Sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
3.77	67.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.303	α = 90
b = 187.303	β = 90
c = 187.303	γ = 90

Symmetry
Space Group	I 2 3

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 PILATUS3 6M		2021-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9762	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.75	76.47	100	0.997	23.5	56.3		28493

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.8			0.962

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	4AIR	2.75	76.466	28475	1448	99.993	0.151	0.1478	0.16	0.2085	0.21	65.938

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.798
r_dihedral_angle_3_deg	19.454
r_lrange_it	16.209
r_lrange_other	16.188
r_scangle_it	14.844
r_scangle_other	14.842
r_dihedral_angle_6_deg	14.811
r_mcangle_it	12.824
r_mcangle_other	12.823
r_scbond_it	11.68
r_scbond_other	11.678
r_mcbond_it	9.789
r_mcbond_other	9.789
r_dihedral_angle_1_deg	8.462
r_angle_refined_deg	2.246
r_angle_other_deg	0.714
r_symmetry_nbd_refined	0.288
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.205
r_nbd_other	0.203
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.176
r_ncsr_local_group_1	0.133
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.088
r_symmetry_xyhbond_nbd_refined	0.035
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4827
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing