Experiment: 2O4M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P6B	PDB ENTRY 1P6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	Zinc acetate 0.2 M, Sodium Cacodylate 0.1 M, PEG MME 12 %, pH 6.5, Vapor diffusion, Hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.759	α = 90.03
b = 68.906	β = 100.29
c = 89.67	γ = 94.12

Symmetry
Space Group	P 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 210		2006-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	1.000	NSLS	X6A

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	1.58	28.33	93.1	0.075	0.06	8.4	1.9	169088	169088

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	1.58	1.64	73.5		0.397	0.334	1.53	1.7	13353

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-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 1P6B	1.64	28.33	155682	7763	95.27	0.192	0.192	0.189	0.1871	0.244	0.2414	RANDOM	19.873

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]
1.25	-0.03	-0.21	-0.6	-0.07	-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.114
r_dihedral_angle_4_deg	19.302
r_dihedral_angle_3_deg	14.129
r_dihedral_angle_1_deg	7.147
r_scangle_it	5.453
r_scbond_it	3.849
r_mcangle_it	2.452
r_mcbond_it	1.879
r_angle_refined_deg	1.56
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.114
r_dihedral_angle_4_deg	19.302
r_dihedral_angle_3_deg	14.129
r_dihedral_angle_1_deg	7.147
r_scangle_it	5.453
r_scbond_it	3.849
r_mcangle_it	2.452
r_mcbond_it	1.879
r_angle_refined_deg	1.56
r_nbtor_refined	0.318
r_chiral_restr	0.302
r_symmetry_vdw_refined	0.275
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.159
r_metal_ion_refined	0.086
r_gen_planes_refined	0.018
r_bond_refined_d	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10075
Nucleic Acid Atoms
Solvent Atoms	1594
Heterogen Atoms	85

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	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.