1YV5 | pdb_00001yv5

Human farnesyl diphosphate synthase complexed with Mg and risedronate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	293	40% PEG 300, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.946	α = 90
b = 110.946	β = 90
c = 70.264	γ = 90

Symmetry
Space Group	P 41 21 2

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		2005-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.16	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	70.2	99.9	0.092	0.092		8.7	30242	30212			34.3

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	2.11	100		2.2	8.6	4319

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 (All)	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	1UBV	2	52.34	28656	28467	1529	99.34	0.20765	0.20765	0.20549	0.21	0.24888	0.25	RANDOM	25.087

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]
-3.2			-3.2		6.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.077
r_dihedral_angle_4_deg	18.511
r_dihedral_angle_3_deg	14.515
r_scangle_it	6.838
r_dihedral_angle_1_deg	5.484
r_scbond_it	5.361
r_mcangle_it	3.248
r_mcbond_it	2.122
r_angle_refined_deg	1.531
r_angle_other_deg	0.824
r_mcbond_other	0.54
r_nbd_refined	0.218
r_nbtor_refined	0.195
r_nbd_other	0.17
r_symmetry_vdw_refined	0.163
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_other	0.151
r_metal_ion_refined	0.142
r_symmetry_hbond_refined	0.132
r_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2650
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing