Experiment: 2A7L

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y6L	PDB ENTRY 1Y6L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	3 M NaCl, 0.1 M bisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.63	52.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.595	α = 90
b = 60.655	β = 90
c = 133.52	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2005-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	25	93.6	0.055	36.68	6.2	27952	27952		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	50.4		0.475	1.94	2.7	1475

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 (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 1Y6L	1.82	24.44	26406	1403	95.15	0.26378	0.26179	0.26	0.29982	0.3	RANDOM	36.259

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]
-2.26			4.09		-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.171
r_dihedral_angle_4_deg	28.118
r_dihedral_angle_3_deg	15.316
r_dihedral_angle_1_deg	5.712
r_scangle_it	5.645
r_scbond_it	3.705
r_mcangle_it	2.774
r_mcbond_it	1.695
r_angle_refined_deg	1.352
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.171
r_dihedral_angle_4_deg	28.118
r_dihedral_angle_3_deg	15.316
r_dihedral_angle_1_deg	5.712
r_scangle_it	5.645
r_scbond_it	3.705
r_mcangle_it	2.774
r_mcbond_it	1.695
r_angle_refined_deg	1.352
r_nbtor_refined	0.309
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.204
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.15
r_metal_ion_refined	0.131
r_chiral_restr	0.096
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1922
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	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.