Experiment: 3HMK

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.261	α = 90
b = 102.96	β = 90
c = 120.923	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2008-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0332	Diamond	I03

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	2.1	41.1	95.8	0.069	0.069	10.1	3.17	34466	32657	2	2	23.8

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)
	2.1	2.18	74.8		0.195	0.195	3.5	1.95	1837

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	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 1FKP	2.1	41.1	2	2	34466	32657	1795	95.77	0.24389	0.24136	0.28949	RANDOM	29.478

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.297
r_dihedral_angle_4_deg	19.152
r_dihedral_angle_3_deg	14.354
r_dihedral_angle_1_deg	5.242
r_scangle_it	1.34
r_angle_refined_deg	0.993
r_scbond_it	0.771
r_mcangle_it	0.739
r_mcbond_it	0.402
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.297
r_dihedral_angle_4_deg	19.152
r_dihedral_angle_3_deg	14.354
r_dihedral_angle_1_deg	5.242
r_scangle_it	1.34
r_angle_refined_deg	0.993
r_scbond_it	0.771
r_mcangle_it	0.739
r_mcbond_it	0.402
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4844
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	32

Software

Software
Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	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.