7ROF | pdb_00007rof

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9-H275E with L-Trp non-covalently bound

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6AM8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.85	298	13-21% PEG3350, 0.1 M HEPES pH 7.85

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.402	α = 90
b = 82.658	β = 90
c = 322.255	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	100	PIXEL	DECTRIS EIGER X 9M		2021-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.033167	APS	21-ID-D

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		fixed target

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.39	50	99.5	0.058	0.998	8.4	13.4		823988

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.39	2.45	99.5		1.548	0.488	0.8	14.1

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	6AM8	2.39	46.695	61584	3098	99.305	0.229	0.2272	0.23	0.2714	0.27	72.415

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]
1.735			5.909		-7.644

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.18
r_dihedral_angle_4_deg	16.624
r_dihedral_angle_3_deg	13.577
r_dihedral_angle_1_deg	6.822
r_lrange_it	2.913
r_lrange_other	2.913
r_mcangle_it	1.293
r_mcangle_other	1.293
r_angle_refined_deg	1.215
r_scangle_it	1.189
r_scangle_other	1.189
r_angle_other_deg	1.165
r_mcbond_it	0.746
r_mcbond_other	0.746
r_scbond_it	0.69
r_scbond_other	0.69
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_refined	0.205
r_nbd_other	0.203
r_nbd_refined	0.176
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.152
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.04
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11078
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing