2O2K | pdb_00002o2k

Crystal Structure of the Activation Domain of Human Methionine Synthase Isoform/Mutant D963E/K1071N

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MSK	PDB entry 1MSK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	0.1M Tris/HCl, 0.1-0.4M sodium acetate, 10-12% PEG 8000, 10-12% PEG 1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.854	α = 90
b = 90.051	β = 90
c = 123.006	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	93	CCD	ADSC QUANTUM 4		2005-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	20	96.3	0.064	20.1	5.3	110417	106145			25.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	96.5		0.402	3.2	5.3	110417

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 1MSK	1.6	19.83	110417	104248	5477	100	0.2113	0.2094	0.21	0.24782	0.25	RANDOM	25.243

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]
			-0.01		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.041
r_dihedral_angle_4_deg	15.643
r_dihedral_angle_3_deg	12.657
r_dihedral_angle_1_deg	5.231
r_scangle_it	2.065
r_scbond_it	1.364
r_angle_refined_deg	1.038
r_mcangle_it	0.923
r_mcbond_it	0.545
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.041
r_dihedral_angle_4_deg	15.643
r_dihedral_angle_3_deg	12.657
r_dihedral_angle_1_deg	5.231
r_scangle_it	2.065
r_scbond_it	1.364
r_angle_refined_deg	1.038
r_mcangle_it	0.923
r_mcbond_it	0.545
r_nbtor_refined	0.306
r_nbd_refined	0.19
r_symmetry_vdw_refined	0.131
r_xyhbond_nbd_refined	0.092
r_symmetry_hbond_refined	0.084
r_chiral_restr	0.072
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5460
Nucleic Acid Atoms
Solvent Atoms	1195
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.