1RQC | pdb_00001rqc

Crystals of peptide deformylase from Plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Tris, sodium chloride, magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.263	α = 90
b = 121.263	β = 90
c = 177.272	γ = 90

Symmetry
Space Group	P 41

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		2001-05-05	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9794, 0.9792, 0.96400	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	25	89.3	0.096	10.6	4.8		77903		-3	53.229

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.64	43.7		0.482	2.2	3.2	4631

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.8	20	49121	49121	2624	82.49	0.22755	0.22493	0.2126	0.27698	0.2616	RANDOM	40.875

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]
0.47			0.47		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.987
r_scangle_it	3.129
r_mcangle_it	2.085
r_scbond_it	1.816
r_angle_refined_deg	1.502
r_mcbond_it	1.076
r_symmetry_hbond_refined	0.334
r_symmetry_vdw_refined	0.307
r_nbd_refined	0.261
r_xyhbond_nbd_refined	0.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.987
r_scangle_it	3.129
r_mcangle_it	2.085
r_scbond_it	1.816
r_angle_refined_deg	1.502
r_mcbond_it	1.076
r_symmetry_hbond_refined	0.334
r_symmetry_vdw_refined	0.307
r_nbd_refined	0.261
r_xyhbond_nbd_refined	0.226
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14339
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
SHARP	phasing
DM	phasing
CNS	refinement

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.