8W33 | pdb_00008w33

Structure of McrD (methyl-coenzyme M reductase operon protein D) from Methanomassiliicoccus luminyensis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	279	MgCl2, CaCl2, MES, imidazole, glycerol, PEG 4000, carboxylic acids mix (formate, acetate, citrate, tartrate, oxamate)

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.062	α = 90
b = 90.224	β = 90
c = 121.415	γ = 90

Symmetry
Space Group	C 2 2 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		2018-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95366	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.65	45.15	100	0.071	0.077	0.029	0.999	16.8	13.7		57078

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	100		2.263	2.437	0.902	0.816	1.6	14

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	FREE R-VALUE	1.65	45.15	57036	2855	99.988	0.178	0.1776	0.19	0.1924	0.2	Random Selection	38.29

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]
-1.905			3.922		-2.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.638
r_dihedral_angle_3_deg	11.722
r_lrange_it	8.133
r_lrange_other	8.084
r_dihedral_angle_2_deg	6.915
r_scangle_it	6.454
r_scangle_other	6.452
r_dihedral_angle_1_deg	6.333
r_scbond_it	4.097
r_scbond_other	4.096
r_mcangle_it	3.684
r_mcangle_other	3.683
r_mcbond_it	2.558
r_mcbond_other	2.557
r_angle_refined_deg	1.507
r_angle_other_deg	0.521
r_nbd_refined	0.212
r_nbd_other	0.191
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.148
r_xyhbond_nbd_refined	0.121
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.077
r_symmetry_nbd_refined	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2275
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
BUCCANEER	model building
CRANK2	phasing