9CBO | pdb_00009cbo

Methionine synthase from Thermus thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8SSC	Fol and Cob domains used as search models

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277.15	25% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
4.21	70.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.769	α = 90
b = 187.769	β = 90
c = 325.547	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 300 mm	K-B pair of biomorph mirrors for vertical and horizontal focusing	2015-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	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	3.34	325.55	99.9	0.24	0.256	0.087	0.986	6.7	8.3		85017

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	3.34	3.4		98.1	2.194	2.333	0.787	0.428		8.4

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 (Observed)	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	3.34	163.18	80679	4226	99.89	0.17532	0.17316	0.1792	0.216	0.2172	RANDOM	118.474

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]
0.48			0.48		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	21.611
r_long_range_B_refined	21.609
r_scangle_other	18.741
r_mcangle_it	16.606
r_mcangle_other	16.606
r_dihedral_angle_3_deg	14.766
r_scbond_it	13.426
r_scbond_other	13.426
r_dihedral_angle_2_deg	12.501
r_mcbond_it	11.838
r_mcbond_other	11.838
r_dihedral_angle_1_deg	6.619
r_angle_refined_deg	2.633
r_angle_other_deg	0.699
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23842
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	588

Software

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