1ZKO

Crystal structure of Glycine cleavage system H protein (tm0212) from Thermotoga maritima at 1.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	4	277	1.0M LiCl, 30.0% PEG-6000, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	33.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.95	α = 90
b = 65.249	β = 90
c = 69.14	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	100	CCD	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2005-04-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.946415, 0.979129, 0.979494	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.56	42.53	87.4	0.073	0.073	6.4	3.6		30875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.64	40		0.367	0.367	2	1.7

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.65	42.53	26956	1433	94.6	0.227	0.22724	0.225	0.27	RANDOM	18.464

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]
0.46			0.49		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.656
r_dihedral_angle_3_deg	12.109
r_dihedral_angle_4_deg	11.897
r_scangle_it	5.864
r_dihedral_angle_1_deg	5.287
r_scbond_it	3.808
r_mcangle_it	2.141
r_mcbond_it	1.209
r_angle_refined_deg	1.065
r_nbtor_refined	0.296

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.656
r_dihedral_angle_3_deg	12.109
r_dihedral_angle_4_deg	11.897
r_scangle_it	5.864
r_dihedral_angle_1_deg	5.287
r_scbond_it	3.808
r_mcangle_it	2.141
r_mcbond_it	1.209
r_angle_refined_deg	1.065
r_nbtor_refined	0.296
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2011
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
autoSHARP	phasing
SHELXL	refinement

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.