Experiment: 3KPM

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	0.2M ammonium acetate, 20-28% PEG 4000, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.705	α = 90
b = 81.868	β = 90
c = 109.814	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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1	APS	23-ID-D

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	1.6	100	93.4	0.067	21.4	3.8		57027

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	1.6	1.66	99		0.472		3.8	5975

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 1SYV	1.6	65.65	56266	2847	92.1	0.203	0.201	0.2	0.241	0.2	RANDOM	26.176

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]
-1.06			-0.61		1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.985
r_dihedral_angle_4_deg	16.196
r_dihedral_angle_3_deg	12.931
r_dihedral_angle_1_deg	5.728
r_scangle_it	2.268
r_scbond_it	1.532
r_angle_refined_deg	1.202
r_mcangle_it	1.008
r_mcbond_it	0.617
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.985
r_dihedral_angle_4_deg	16.196
r_dihedral_angle_3_deg	12.931
r_dihedral_angle_1_deg	5.728
r_scangle_it	2.268
r_scbond_it	1.532
r_angle_refined_deg	1.202
r_mcangle_it	1.008
r_mcbond_it	0.617
r_nbtor_refined	0.303
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.119
r_xyhbond_nbd_refined	0.111
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3169
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	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.