Experiment: 2PBD

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277.15	150mM DL-malic acid pH 7.0, 18% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.094	α = 90
b = 56.589	β = 104.75
c = 75.227	γ = 90

Symmetry
Space Group	C 1 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	200	CCD	ADSC QUANTUM 315	mirrors	2006-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	1.5	50	97.5	0.071	0.071	41.9	7.3	75393	75393			10.87

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	1.5	1.55	98.3		0.293	0.293	9	7.5	7487

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2PAV	1.501	31.77	76665	76665	3855	99.06	0.158	0.158	0.156	0.19	RANDOM	10.847

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]
0.04		0.09	-0.08		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.582
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	13.356
r_dihedral_angle_1_deg	6.447
r_scangle_it	4.118
r_scbond_it	2.788
r_mcangle_it	1.737
r_angle_refined_deg	1.695
r_mcbond_it	1.138
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.582
r_dihedral_angle_4_deg	17.353
r_dihedral_angle_3_deg	13.356
r_dihedral_angle_1_deg	6.447
r_scangle_it	4.118
r_scbond_it	2.788
r_mcangle_it	1.737
r_angle_refined_deg	1.695
r_mcbond_it	1.138
r_nbtor_refined	0.317
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.173
r_metal_ion_refined	0.133
r_chiral_restr	0.11
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4049
Nucleic Acid Atoms
Solvent Atoms	732
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
AMoRE	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.