Experiment: 1YQB

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	2M(NH4)2SO4, 0.1M bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.913	α = 90
b = 41.913	β = 90
c = 94.442	γ = 90

Symmetry
Space Group	P 43 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++		2005-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	1.5418

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	2	30	99.7	0.061	35.1		6167	6167		-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)
	2	2.07	97.3		0.42	2.92

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1XD3	2	30	6127	6126	276	99.67	0.18725	0.18487	0.23993	RANDOM	33.114

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]
-0.08			-0.08		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.178
r_dihedral_angle_4_deg	22.338
r_dihedral_angle_3_deg	14.686
r_dihedral_angle_1_deg	6.33
r_scangle_it	5.324
r_scbond_it	3.21
r_mcangle_it	1.969
r_angle_refined_deg	1.801
r_mcbond_it	1.238
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.178
r_dihedral_angle_4_deg	22.338
r_dihedral_angle_3_deg	14.686
r_dihedral_angle_1_deg	6.33
r_scangle_it	5.324
r_scbond_it	3.21
r_mcangle_it	1.969
r_angle_refined_deg	1.801
r_mcbond_it	1.238
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.297
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.105
r_bond_refined_d	0.021
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	689
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	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 R01GM133198.