8SSE | pdb_00008sse

Methionine synthase, C-terminal fragment, Cobalamin and Reactivation Domains from Thermus thermophilus HB8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BUL	Minus Cap Domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277.15	0.1 M Bis-Tris Propane, pH 7, 60% v/v Tacismate, pH 7, 5% PEG 300, 10% ethylene glycol, 1.5 mM cyanocobalamin

Crystal Properties
Matthews coefficient	Solvent content
2.7	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.135	α = 90
b = 95.844	β = 91.956
c = 238.745	γ = 90

Symmetry
Space Group	C 1 2 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	K-B pair of biomorph mirrors for vertical and horizontal focusing	2022-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033	APS	23-ID-B

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	3.15	49.295	98.9	0.192	0.228	0.121	0.989	4.6	3.5		64421

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	3.15	3.23		99.4	0.973	1.152	0.609	0.583		3.5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3bul	3.15	49.295	64409	3279	98.691	0.248	0.2453	0.25	0.3067	0.3	RANDOM	82.81

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]
-1.308		-2.874	-0.296		1.796

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	21.946
r_lrange_it	21.943
r_dihedral_angle_6_deg	16.006
r_dihedral_angle_3_deg	15.674
r_scangle_it	13.54
r_scangle_other	13.54
r_mcangle_it	13.224
r_mcangle_other	13.224
r_dihedral_angle_2_deg	11.121
r_scbond_it	8.404
r_scbond_other	8.404
r_mcbond_it	8.37
r_mcbond_other	8.369
r_dihedral_angle_1_deg	7.18
r_angle_refined_deg	1.929
r_angle_other_deg	1.019
r_symmetry_xyhbond_nbd_refined	0.162
r_nbd_refined	0.148
r_nbtor_refined	0.148
r_symmetry_nbd_other	0.133
r_nbd_other	0.133
r_symmetry_nbd_refined	0.127
r_chiral_restr_other	0.115
r_xyhbond_nbd_refined	0.111
r_ncsr_local_group_14	0.101
r_ncsr_local_group_5	0.098
r_ncsr_local_group_9	0.098
r_ncsr_local_group_10	0.097
r_ncsr_local_group_12	0.097
r_ncsr_local_group_6	0.096
r_ncsr_local_group_15	0.096
r_ncsr_local_group_1	0.094
r_ncsr_local_group_3	0.094
r_chiral_restr	0.093
r_ncsr_local_group_7	0.093
r_ncsr_local_group_8	0.092
r_ncsr_local_group_2	0.089
r_ncsr_local_group_4	0.089
r_ncsr_local_group_11	0.089
r_ncsr_local_group_13	0.088
r_symmetry_nbtor_other	0.066
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_symmetry_xyhbond_nbd_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	24040
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	546

Software

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