Experiment: 2FTP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YDN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1M Tris 8.0, 3.4M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
4.41	72.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.012	α = 90
b = 189.012	β = 90
c = 189.012	γ = 90

Symmetry
Space Group	I 4 3 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	MARRESEARCH	xenocs multilayer confocal mirror	2005-03-11	M	SINGLE WAVELENGTH

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

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	2.4	80	99.6	0.086	0.086	12.7	42.6	22088	21999

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	2.4	2.44	100		0.53	0.53	9.97	42.6	1126

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YDN	2.4	80	22088	21999	735	99.6	0.18799	0.18799	0.18713	0.19	0.21309	0.17	RANDOM	36.229

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.109
r_dihedral_angle_3_deg	18.507
r_dihedral_angle_4_deg	18.488
r_dihedral_angle_1_deg	8.317
r_scangle_it	3.581
r_scbond_it	2.139
r_angle_refined_deg	1.432
r_mcangle_it	1.202
r_mcbond_it	0.61
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.109
r_dihedral_angle_3_deg	18.507
r_dihedral_angle_4_deg	18.488
r_dihedral_angle_1_deg	8.317
r_scangle_it	3.581
r_scbond_it	2.139
r_angle_refined_deg	1.432
r_mcangle_it	1.202
r_mcbond_it	0.61
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.175
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.126
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2238
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
ARP/wARP	model building

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.