9HQI | pdb_00009hqi

T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P4(3)2(1)2(1)]

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9HQD

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.81	α = 90
b = 131.81	β = 90
c = 128.43	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		2022-12-01	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	2.1	30	96.6	0.058	13.3	3.8		64130

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.2	97.9		0.595	2	3.5

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	2.1	30	60902	3206	96.56	0.17206	0.17044	0.1818	0.20136	0.2112	RANDOM	44.143

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]
-0.35			-0.35		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.597
r_dihedral_angle_4_deg	15.402
r_dihedral_angle_3_deg	13.766
r_dihedral_angle_1_deg	4.431
r_long_range_B_refined	4.197
r_long_range_B_other	4.046
r_scangle_other	3.109
r_mcangle_it	3.046
r_mcangle_other	3.045
r_scbond_it	2.317
r_scbond_other	2.317
r_mcbond_it	2.16
r_mcbond_other	2.16
r_angle_other_deg	1.153
r_angle_refined_deg	1.152
r_rigid_bond_restr	0.688
r_chiral_restr	0.05
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4939
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	110

Software

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