Experiment: 3B75

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	277	PEG 4000, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 237.987	α = 90
b = 59.267	β = 125.36
c = 137.024	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	120	CCD			2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.95400	SLS	X06SA

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	2.3	15	92.3	0.034	0.034	23.7	3.2		64184			39

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)
	2.3	2.38	71		0.391	0.391	2.5

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 1HHO	2.3	14.9	60718	3020	87.33	0.249	0.244	0.2426	0.331	0.3284	RANDOM	57.868

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]
-3.08		-1.95	3.36		-2.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.848
r_dihedral_angle_3_deg	19.165
r_dihedral_angle_4_deg	16.003
r_dihedral_angle_1_deg	6.193
r_scangle_it	2.347
r_angle_refined_deg	1.755
r_scbond_it	1.591
r_mcangle_it	1.115
r_mcbond_it	0.63
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.848
r_dihedral_angle_3_deg	19.165
r_dihedral_angle_4_deg	16.003
r_dihedral_angle_1_deg	6.193
r_scangle_it	2.347
r_angle_refined_deg	1.755
r_scbond_it	1.591
r_mcangle_it	1.115
r_mcbond_it	0.63
r_nbtor_refined	0.293
r_symmetry_hbond_refined	0.28
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.158
r_chiral_restr	0.108
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10950
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	513

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.