8TFO | pdb_00008tfo

Structure of MKvar

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.4	293	Protein bound to mevalonate at about 3 mg/mL was set up in 150 nL plus 150 nL drops over 50 microlitres of reservoir which contained: 0.126 M calcium acetate, 24.9 v/v PEG 400, 0.09 M sodium HEPES pH 8.4 with 10 mM taurine

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.081	α = 90
b = 80.705	β = 90
c = 207.467	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		2020-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953723	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	45.1	99.8	0.292	0.057	0.999	11.8	27.1		52511

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	97.5		4.656	0.9	0.623	1	26.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	44.091	52296	2598	99.979	0.21	0.2079	0.22	0.2471	0.25	41.413

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]
2.539			1.818		-4.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.353
r_dihedral_angle_3_deg	15.159
r_dihedral_angle_2_deg	9.415
r_lrange_other	8.847
r_lrange_it	8.842
r_dihedral_angle_1_deg	6.357
r_scangle_it	5.897
r_scangle_other	5.896
r_mcangle_it	4.712
r_mcangle_other	4.712
r_scbond_it	3.781
r_scbond_other	3.78
r_mcbond_it	3.108
r_mcbond_other	3.108
r_angle_refined_deg	1.262
r_angle_other_deg	0.431
r_nbd_other	0.213
r_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.159
r_symmetry_nbd_refined	0.121
r_ncsr_local_group_1	0.116
r_symmetry_nbtor_other	0.076
r_symmetry_metal_ion_refined	0.073
r_symmetry_xyhbond_nbd_other	0.067
r_chiral_restr	0.058
r_xyhbond_nbd_other	0.02
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5885
Nucleic Acid Atoms
Solvent Atoms	151
Heterogen Atoms	35

Software

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