9NZY | pdb_00009nzy

Structure of Methanogen MtxX (Methanogen Marker Protein MMP4) from Methanothermobacter thermautotrophicus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	0.1 M Na HEPES pH 7.5, 10% w/v PEG 8000, 8% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.21	44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.484	α = 90
b = 72.31	β = 96.115
c = 65.58	γ = 90

Symmetry
Space Group	P 1 21 1

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	Si mirrors with Rh stripes	2017-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953653	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	65.29	100	0.071	0.027	1	15.4	6.3		69258			24.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	99.6		1	0.48	0.78	1	4.3

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	1.6	65.29	69236	3507	99.951	0.164	0.1628	0.1628	0.185	0.1848	Random selection	36.75

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]
-0.313		0.84	-0.612		0.728

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.132
r_dihedral_angle_3_deg	13.81
r_lrange_it	8.47
r_lrange_other	8.435
r_dihedral_angle_2_deg	7.829
r_scangle_it	6.49
r_scangle_other	6.489
r_dihedral_angle_1_deg	6.288
r_scbond_it	4.202
r_scbond_other	4.201
r_mcangle_it	3.875
r_mcangle_other	3.875
r_mcbond_it	2.665
r_mcbond_other	2.664
r_angle_refined_deg	1.721
r_angle_other_deg	0.605
r_nbd_refined	0.223
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.164
r_nbd_other	0.142
r_symmetry_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3565
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
CRANK2	phasing