Experiment: 2QYJ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MJO	PDB entry 1MJO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	2.7M (NH4)2SO4, 0.1M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.48	α = 90
b = 74.48	β = 90
c = 50.99	γ = 120

Symmetry
Space Group	P 61

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	MAR scanner 345 mm plate	mirror	2005-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.54179

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	64.55	92.8	0.068	0.073	21.44	7.68		10232		-3	31.966

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	2.1	48.1		0.337	0.364	6.2	7.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1MJO	2.05	64.55	10232	10204	493	99.76	0.188	0.188	0.186	0.18	0.226	0.22	RANDOM	26.279

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]
1.02	0.51		1.02		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.102
r_dihedral_angle_4_deg	18.793
r_dihedral_angle_3_deg	14.197
r_dihedral_angle_1_deg	4.798
r_scangle_it	2.931
r_scbond_it	1.889
r_angle_refined_deg	1.109
r_mcangle_it	1.106
r_mcbond_it	0.642
r_nbtor_refined	0.298

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.102
r_dihedral_angle_4_deg	18.793
r_dihedral_angle_3_deg	14.197
r_dihedral_angle_1_deg	4.798
r_scangle_it	2.931
r_scbond_it	1.889
r_angle_refined_deg	1.109
r_mcangle_it	1.106
r_mcbond_it	0.642
r_nbtor_refined	0.298
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.206
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1161
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

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.