Experiment: 2PBN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HY3	PDB entry 2HY3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100mM Sodium MES pH 6.5, 22% PEG 8000, 200mM Ammonium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.338	α = 90
b = 107.338	β = 90
c = 67.757	γ = 120

Symmetry
Space Group	P 32 2 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 315		2006-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.10000	NSLS	X29A

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	1.7	53.683	99.8	0.054	0.054	16.1	10.2	49677	49677			31.3

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)
	1.7	1.79	99		0.645	0.645	2.2	7.3	7108

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 2HY3	1.7	20	49610	49610	2485	99.83	0.209	0.208	0.234	RANDOM	41.844

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]
-0.63	-0.31		-0.63		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.267
r_dihedral_angle_4_deg	16.741
r_dihedral_angle_3_deg	13.437
r_dihedral_angle_1_deg	5.466
r_scangle_it	4.865
r_scbond_it	3.075
r_mcangle_it	1.948
r_angle_refined_deg	1.527
r_mcbond_it	1.283
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.267
r_dihedral_angle_4_deg	16.741
r_dihedral_angle_3_deg	13.437
r_dihedral_angle_1_deg	5.466
r_scangle_it	4.865
r_scbond_it	3.075
r_mcangle_it	1.948
r_angle_refined_deg	1.527
r_mcbond_it	1.283
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2330
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling

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.