Experiment: 3DPH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BUO	PDB ENTRY 2BUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	7.5	292	30% PEG4000, 100mM NaHEPES, 200mM CaCl2, pH 7.5, EVAPORATION, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.839	α = 90
b = 74.909	β = 99.98
c = 32.708	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	CCD	MARMOSAIC 225 mm CCD	Dynamically bendable mirror	2007-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.044	SLS	X06SA

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	2	37.4	98.9	0.04	27.2	3.6	9396	9396			16.4

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)
	2	2.07	91.8		0.094	0.094	8.9	2.5	869

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	PDB ENTRY 2BUO	2.01	37.45	8931	8931	447	98.58	0.191	0.191	0.18784	0.19	0.25394	0.25	RANDOM	16.922

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]
-0.07		0.13	-0.07		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.821
r_dihedral_angle_4_deg	18.63
r_dihedral_angle_3_deg	15.022
r_dihedral_angle_1_deg	10.874
r_scangle_it	5.959
r_scbond_it	3.609
r_mcangle_it	2.325
r_angle_refined_deg	1.941
r_mcbond_it	1.259
r_chiral_restr	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.821
r_dihedral_angle_4_deg	18.63
r_dihedral_angle_3_deg	15.022
r_dihedral_angle_1_deg	10.874
r_scangle_it	5.959
r_scbond_it	3.609
r_mcangle_it	2.325
r_angle_refined_deg	1.941
r_mcbond_it	1.259
r_chiral_restr	0.12
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1241
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
RemDAq	data collection
XDS	data reduction
SCALA	data scaling
PHASER	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.