Experiment: 2DPJ

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.059	α = 90
b = 98.059	β = 90
c = 203.102	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	ADSC QUANTUM 210		2005-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	2.3	50	99.3	0.046	45.6	10.5		26535

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)
1	2.3				0.283	8.9

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 (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 2ALZ	2.3	36.76	22903	1964	93.99	0.2412	0.23805	0.23	0.277	0.27	RANDOM	38.591

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]
0.61	0.3		0.61		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.612
r_scangle_it	6.179
r_scbond_it	4.307
r_mcangle_it	3.143
r_angle_refined_deg	2.865
r_mcbond_it	1.796
r_symmetry_vdw_refined	0.365
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.3
r_xyhbond_nbd_refined	0.218

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.612
r_scangle_it	6.179
r_scbond_it	4.307
r_mcangle_it	3.143
r_angle_refined_deg	2.865
r_mcbond_it	1.796
r_symmetry_vdw_refined	0.365
r_symmetry_hbond_refined	0.31
r_nbd_refined	0.3
r_xyhbond_nbd_refined	0.218
r_chiral_restr	0.197
r_bond_refined_d	0.037
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2876
Nucleic Acid Atoms	323
Solvent Atoms	127
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	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 R01GM157729.