4RXD | pdb_00004rxd

T. Brucei Farnesyl Diphosphate Synthase Complexed with Risedronate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OGD	PDB ENTRY 2OGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.75	298	10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.34	α = 90
b = 90.305	β = 89.91
c = 88.709	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 300 mm CCD		2008-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	99.8			82972		1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	99.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2OGD	2	29.55	82966	78824	4142	99.69	0.2132	0.2112	0.2508	0.24	RANDOM	28.582

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]
0.13		0.08			-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.098
r_dihedral_angle_4_deg	17.537
r_dihedral_angle_3_deg	15.396
r_dihedral_angle_1_deg	4.489
r_scangle_it	2.596
r_scbond_it	1.709
r_angle_refined_deg	1.203
r_mcangle_it	1.152
r_mcbond_it	0.721
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.087
r_bond_refined_d	0.01
r_metal_ion_refined	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8547
Nucleic Acid Atoms
Solvent Atoms	484
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing