Experiment: 2PMN

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PML	PfPK7 in complex with ATP analogue (2PML)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	300	0.1 M Hepes pH7.5; 20% PEG10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.406	α = 90
b = 82.084	β = 90
c = 138.962	γ = 90

Symmetry
Space Group	C 2 2 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 4		2006-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

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	2.75	20	97.7	0.066	15.8	3.7		10971	2	2

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	2.8	2.871	87.3		0.461	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PfPK7 in complex with ATP analogue (2PML)	2.8	20	2	10971	9946	499	98.22	0.22277	0.2192	0.21	0.29559	0.29	RANDOM	38.814

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]
3.27			-0.57		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.25
r_dihedral_angle_3_deg	19.621
r_dihedral_angle_4_deg	18.543
r_dihedral_angle_1_deg	6.81
r_angle_refined_deg	1.309
r_scangle_it	1.24
r_mcangle_it	0.839
r_scbond_it	0.762
r_mcbond_it	0.463
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.25
r_dihedral_angle_3_deg	19.621
r_dihedral_angle_4_deg	18.543
r_dihedral_angle_1_deg	6.81
r_angle_refined_deg	1.309
r_scangle_it	1.24
r_mcangle_it	0.839
r_scbond_it	0.762
r_mcbond_it	0.463
r_nbtor_refined	0.317
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.197
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.097
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2856
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	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.