9HQD | pdb_00009hqd

T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P2(1)2(1)2(1)]

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.1 M Tris; 0.05 M MgCl2; 25% PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.43	α = 90
b = 75.13	β = 90
c = 134.18	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		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	30	98.1	0.059	12.4	4.1		56395

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	99.8		0.679		4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	30	53506	2816	98.08	0.1846	0.1826	0.1926	0.2193	0.2285	RANDOM	39.232

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]
2.02			0.7		-2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.145
r_dihedral_angle_4_deg	15.68
r_dihedral_angle_3_deg	14.314
r_dihedral_angle_1_deg	4.813
r_angle_refined_deg	1.159
r_angle_other_deg	1.157
r_rigid_bond_restr	0.578
r_chiral_restr	0.049
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.145
r_dihedral_angle_4_deg	15.68
r_dihedral_angle_3_deg	14.314
r_dihedral_angle_1_deg	4.813
r_angle_refined_deg	1.159
r_angle_other_deg	1.157
r_rigid_bond_restr	0.578
r_chiral_restr	0.049
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
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	173
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.