Experiment: 3HLW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P74	PDB entry 2P74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	293	0.8M phosphate , pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.104	α = 90
b = 106.564	β = 101.92
c = 47.503	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	ADSC QUANTUM 315r	MIRROR	2008-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	89	0.059	13.6	3.6		62304			14.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	99.6		0.64	11.5	3.9	6928

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB entry 2P74	1.5	5	2	59132	3153	91.48	0.16199	0.16003	0.19855	RANDOM	12.195

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	40.012
r_dihedral_angle_4_deg	13.657
r_dihedral_angle_3_deg	12.844
r_dihedral_angle_1_deg	4.319
r_scangle_it	3.829
r_scbond_it	2.513
r_angle_refined_deg	1.892
r_mcangle_it	1.625
r_mcbond_it	0.995
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.012
r_dihedral_angle_4_deg	13.657
r_dihedral_angle_3_deg	12.844
r_dihedral_angle_1_deg	4.319
r_scangle_it	3.829
r_scbond_it	2.513
r_angle_refined_deg	1.892
r_mcangle_it	1.625
r_mcbond_it	0.995
r_nbtor_refined	0.31
r_nbd_refined	0.252
r_symmetry_vdw_refined	0.223
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.085
r_gen_planes_refined	0.011
r_bond_refined_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3895
Nucleic Acid Atoms
Solvent Atoms	666
Heterogen Atoms	120

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.