7RNP | pdb_00007rnp

Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9_H275E with 4-Cl-Trp non-covalently bound

X-RAY DIFFRACTION

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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 and 0.1 M Na HEPES pH 7.85

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.162	α = 90
b = 81.198	β = 90
c = 321.014	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 16M		2021-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03317	APS	23-ID-B

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	2.25	40.003	98.8	0.046	0.998	8.8	13.4		69911

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	2.25	2.3			0.825	0.703	1.1

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	2.25	40.003	69895	3482	98.448	0.229	0.2273	0.23	0.2666	0.26	63.805

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]
-0.161			3.811		-3.649

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.963
r_dihedral_angle_3_deg	13.142
r_dihedral_angle_4_deg	12.377
r_dihedral_angle_1_deg	6.592
r_lrange_it	3.119
r_lrange_other	3.116
r_chiral_restr_other	1.795
r_scangle_it	1.485
r_scangle_other	1.485
r_mcangle_it	1.432
r_mcangle_other	1.432
r_angle_refined_deg	1.202
r_angle_other_deg	1.178
r_scbond_it	0.901
r_scbond_other	0.901
r_mcbond_other	0.873
r_mcbond_it	0.872
r_symmetry_xyhbond_nbd_refined	0.275
r_nbd_other	0.196
r_symmetry_nbd_other	0.179
r_nbd_refined	0.174
r_nbtor_refined	0.152
r_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.127
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.042
r_gen_planes_refined	0.005
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11156
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	36

Software

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