Experiment: 2PBC

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	32% PEG MME550, CRYOPROTECTED IN PARATONE-N, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.43	α = 90
b = 39.335	β = 91.28
c = 108.316	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	IMAGE PLATE	RIGAKU RAXIS IV++		2006-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	23.1	98.5	0.044	27.8	3.4	32970	32970		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	85.3		0.155	7.8	3	2860

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1Y0O	1.8	23.06	31311	1648	98.32	0.18861	0.18493	0.25986	RANDOM	21.157

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]
0.46		-0.12	-0.92		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.077
r_dihedral_angle_3_deg	15.201
r_dihedral_angle_4_deg	11.665
r_dihedral_angle_1_deg	7.078
r_scangle_it	4.06
r_scbond_it	3.098
r_mcangle_it	2.083
r_angle_refined_deg	1.687
r_mcbond_it	1.474
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.077
r_dihedral_angle_3_deg	15.201
r_dihedral_angle_4_deg	11.665
r_dihedral_angle_1_deg	7.078
r_scangle_it	4.06
r_scbond_it	3.098
r_mcangle_it	2.083
r_angle_refined_deg	1.687
r_mcbond_it	1.474
r_nbtor_refined	0.313
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.21
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.122
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3123
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.