Experiment: 2PMO

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	300	0.1 M Hepes pH7.5; 20% PEG 10K, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.061	α = 90
b = 82.473	β = 90
c = 138.717	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		2005-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.9310	ESRF	ID14-3

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	2.9	69.34	99.7	0.096	11	3.6		9580	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	2.9	2.975	100		0.478	2.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PfPK7 in complex with an ATP analogue (2PML)	2.9	69.34	2	9580	9098	460	99.5	0.23453	0.23044	0.3158	RANDOM	36.177

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]
3.82			-1.77		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.002
r_dihedral_angle_3_deg	19.846
r_dihedral_angle_4_deg	14.83
r_dihedral_angle_1_deg	6.018
r_angle_refined_deg	1.375
r_scangle_it	0.842
r_mcangle_it	0.581
r_scbond_it	0.574
r_mcbond_it	0.327
r_nbtor_refined	0.314

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.002
r_dihedral_angle_3_deg	19.846
r_dihedral_angle_4_deg	14.83
r_dihedral_angle_1_deg	6.018
r_angle_refined_deg	1.375
r_scangle_it	0.842
r_mcangle_it	0.581
r_scbond_it	0.574
r_mcbond_it	0.327
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.177
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2856
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	19

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 R01GM133198.