7CAV | pdb_00007cav

Versatile cis-prenyltransferase MM_0014 from Methanosarcina mazei (crystal type: co-FG+DMAPP)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7CAQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.075 M succinic acid, pH7.0, 11% PEG 3350, and 25% glycerol, 3 mM farnesyl pyrophosphate (FPP), 0.3 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.853	α = 90
b = 98.91	β = 90
c = 193.853	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 PILATUS3 S 6M		2018-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.91	48.46	100	0.688	33.6	22.3		147512

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.94			2.05	0.688

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	7CAQ	1.91	47.92	147470	7541	99.814	0.197	0.1963	0.2	0.2195	0.23	42.591

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]
0.005			0.007		-0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.609
r_dihedral_angle_4_deg	20.898
r_dihedral_angle_3_deg	15.048
r_dihedral_angle_1_deg	6.388
r_lrange_it	6.197
r_lrange_other	6.185
r_scangle_it	4.317
r_scangle_other	4.3
r_mcangle_it	3.559
r_mcangle_other	3.559
r_scbond_it	2.877
r_scbond_other	2.844
r_mcbond_it	2.581
r_mcbond_other	2.581
r_angle_other_deg	2.263
r_angle_refined_deg	1.306
r_symmetry_nbd_other	0.219
r_nbd_other	0.201
r_nbd_refined	0.197
r_symmetry_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.125
r_symmetry_xyhbond_nbd_other	0.071
r_chiral_restr	0.063
r_symmetry_nbtor_other	0.062
r_metal_ion_refined	0.055
r_bond_other_d	0.034
r_gen_planes_other	0.007
r_bond_refined_d	0.005
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13896
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	272

Software

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