3K6W | pdb_00003k6w

Apo and ligand bound structures of ModA from the archaeon Methanosarcina acetivorans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	2.1M ammonium sulfate, 3% (v/v) isopropanol with final concentration of sodium molybdate at 125 mM in the drop, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2	VAPOR DIFFUSION, HANGING DROP	8	293	2.1M ammonium sulfate, 1% (v/v) isopropanol with final concentration of sodium molybdate at 125 mM in the drop, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.512	α = 90
b = 66.12	β = 95.99
c = 61.46	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	CCD	ADSC QUANTUM 315		2007-04-30		SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2007-04-30		SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2
2	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.000	ALS	8.2.2

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
1,2	2.45	54.07	93.7	0.082	0.071	13.9	3.5		13167

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)
1,2	2.45	2.54	91.4		0.479	0.431	2	3.3	1265

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	2.45	54.07	13107	681	93.79	0.208	0.207	0.2	0.229	0.23	RANDOM	37.046

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]
-2.51		-3.43	2.06		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.305
r_dihedral_angle_4_deg	13.143
r_dihedral_angle_3_deg	13.054
r_dihedral_angle_1_deg	4.851
r_scangle_it	3.036
r_mcangle_it	2.918
r_scbond_it	2.128
r_mcbond_it	1.803
r_angle_refined_deg	1.727
r_chiral_restr	0.101

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.305
r_dihedral_angle_4_deg	13.143
r_dihedral_angle_3_deg	13.054
r_dihedral_angle_1_deg	4.851
r_scangle_it	3.036
r_mcangle_it	2.918
r_scbond_it	2.128
r_mcbond_it	1.803
r_angle_refined_deg	1.727
r_chiral_restr	0.101
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2416
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

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.