Experiment: 4HBD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		UNPUBLISHED MODEL OF SAME PROTEIN BUT DIFFERENT CRYSTAL DIMENSIONS (P21212; A,B,C=61.46,63.59,163.08 FOR DERIVATIVE (IODIDE?, DIFFRACTION INTENSITIES INCLUDED). THAT STRUCTURE WAS SOLVED WITH SHELX, SIRAS (ISOMORPHOUS ""NATIVE"" DATA NOT PROVIDED AS SAD DOES ALSO WORK)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	20% PEG 3350, 0.2 M ammonium nitrate, VAPOR DIFFUSION, temperature 291K
2	VAPOR DIFFUSION, SITTING DROP		291	20% PEG 3350, 0.2 M ammonium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.061	α = 90
b = 65.568	β = 90
c = 28.758	γ = 90

Symmetry
Space Group	P 21 21 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	RAYONIX MX-300		2012-09-19	M	SINGLE WAVELENGTH
2	2	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2012-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1
2	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.72	75.031	100	0.072	17.7	7.1	31276	31276

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	1.72	1.81	100		0.961	0.961	0.8	7.3	4483

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	UNPUBLISHED MODEL OF SAME PROTEIN BUT DIFFERENT CRYSTAL DIMENSIONS (P21212; A,B,C=61.46,63.59,163.08 FOR DERIVATIVE (IODIDE?, DIFFRACTION INTENSITIES INCLUDED). THAT STRUCTURE WAS SOLVED WITH SHELX, SIRAS (ISOMORPHOUS "NATIVE" DATA NOT PROVIDED AS SAD DOES ALSO WORK)	1.72	37.54	31215	1583	99.98	0.1781	0.1765	0.2072	RANDOM	29.6186

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]
-1.15			1.71		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.199
r_dihedral_angle_4_deg	17.291
r_dihedral_angle_3_deg	12.65
r_dihedral_angle_1_deg	4.854
r_angle_refined_deg	1.524
r_angle_other_deg	0.824
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.199
r_dihedral_angle_4_deg	17.291
r_dihedral_angle_3_deg	12.65
r_dihedral_angle_1_deg	4.854
r_angle_refined_deg	1.524
r_angle_other_deg	0.824
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1849
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
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.