4P7M | pdb_00004p7m

Crystal structure of Plasmodium falciparum MIF in complex with 3-[(2-methyl-6-phenylpyridin-4-yl)oxy]phenol

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	2 M ammonium sulphate, 0.1 M NaCl, 0.1 M Tris.HCl pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.036	α = 90
b = 79.75	β = 90
c = 97.082	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++		2013-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	3.02	50	96.8	0.078	13.5	5		6087

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	3.02	3.07	98.7		0.301		5.1	312

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	3.02	25.02	6077	280	96.16	0.2505	0.2467	0.26	0.3243	0.32	RANDOM	48.283

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]
-0.03			0.17		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.129
r_dihedral_angle_3_deg	15.082
r_dihedral_angle_4_deg	11.57
r_dihedral_angle_1_deg	7.222
r_mcangle_it	5.814
r_mcbond_it	3.659
r_mcbond_other	3.655
r_angle_refined_deg	1.467
r_angle_other_deg	1.144
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.129
r_dihedral_angle_3_deg	15.082
r_dihedral_angle_4_deg	11.57
r_dihedral_angle_1_deg	7.222
r_mcangle_it	5.814
r_mcbond_it	3.659
r_mcbond_other	3.655
r_angle_refined_deg	1.467
r_angle_other_deg	1.144
r_chiral_restr	0.073
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2091
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	21

Software

Software
Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
DENZO	data reduction
SCALEPACK	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.