Experiment: 3KYR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DM6	PDB ENTRY 3DM6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	299	16% PEG8000, 0.1M Citrate, 0.3M Lithium sulphate, 0.1M Sodium Chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.762	α = 90
b = 102.774	β = 102.9
c = 101.427	γ = 90

Symmetry
Space Group	P 1 21 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 1	mirrors	2008-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.07225	ESRF	ID23-1

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	2.6	99.015	91.9	0.114	0.114	7.3	2.7		46304	2	2	43.66

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)
	2.6	2.74	93.7		0.386	0.386	1.7	2.7	6868

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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 3DM6	2.6	99.01	2	2	46304	45951	2320	100	0.21	0.21	0.207	0.21	0.269	0.27	RANDOM	24.289

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]
0.02		-0.03	0.11		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.073
r_dihedral_angle_4_deg	19.848
r_dihedral_angle_3_deg	18.383
r_dihedral_angle_1_deg	7.294
r_scangle_it	3.298
r_scbond_it	2.059
r_angle_refined_deg	1.659
r_mcangle_it	1.621
r_mcbond_it	0.957
r_nbtor_refined	0.322

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.073
r_dihedral_angle_4_deg	19.848
r_dihedral_angle_3_deg	18.383
r_dihedral_angle_1_deg	7.294
r_scangle_it	3.298
r_scbond_it	2.059
r_angle_refined_deg	1.659
r_mcangle_it	1.621
r_mcbond_it	0.957
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.264
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.154
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8570
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	156

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	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.