4C81 | pdb_00004c81

IspF (Plasmodium falciparum) CDP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GX1	PDB ENTRY 1GX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	PROTEIN WAS CRYSTALLISED BY HANGING-DROP VAPOUR DIFFUSION. PFISPF SAMPLE IN 100 MM KCL, 100 MM L-ARGININE, 2 MM MGCL2, 50 MM CHES, PH 9.5; WAS CONCENTRATED TO 6 MG/ML, AND HAD CDP DISODIUM SALT ADDED (2 MM FINAL CONCENTRATION). CRYSTALS WERE OBTAINED BY MIXING 2 MICROLITES OF PROTEIN WITH 2 MICROLITRES OF RESERVOIR SOLUTION AT 20 DEGREES C. RESERVOIR SOLUTION: 1.8-2.5 M (NH4)2SO4, 5MM ZNCL2, 100 MM BIS-TRIS, PH 5.5. SATURATED SUCROSE WAS USED AS A CRYO-PROTECTANT DURING COLLECTION.

Crystal Properties
Matthews coefficient	Solvent content
3.4	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.864	α = 90
b = 84.864	β = 90
c = 101.031	γ = 120

Symmetry
Space Group	H 3

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 315r		2009-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	41.63	99.4	0.09	11.1	5.1		35607		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	1.6	1.69	99.3		0.42	2.6	3.3

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 1GX1	1.56	26.38	33786	1810	92.01	0.14506	0.14398	0.16	0.16503	0.18	RANDOM	22.949

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]
0.8			0.8		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.391
r_scangle_it	18.907
r_dihedral_angle_4_deg	13.944
r_scbond_it	13.774
r_dihedral_angle_3_deg	11.696
r_mcangle_it	7.993
r_mcbond_it	5.638
r_dihedral_angle_1_deg	4.905
r_mcbond_other	1.569
r_angle_refined_deg	0.967
r_angle_other_deg	0.761
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1213
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	35

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing