1YQ7

Human farnesyl diphosphate synthase complexed with 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	IMAGE PLATE	RIGAKU RAXIS HTC		2005-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E	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	2.2	55.5	98.9	0.085	15.8	6.1	22156	21912

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	2.32	98.9		2	3	3033

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1UBV	2.2	52.34	21654	21373	1155	98.7	0.22417	0.22152	0.23	0.27381	0.28	RANDOM	19.11

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]
-3.7			-3.7		7.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.994
r_dihedral_angle_4_deg	19.521
r_dihedral_angle_3_deg	17.242
r_scangle_it	6.64
r_dihedral_angle_1_deg	6.078
r_scbond_it	5.326
r_mcangle_it	3.258
r_mcbond_it	2.215
r_angle_refined_deg	1.574
r_angle_other_deg	0.834
r_mcbond_other	0.528
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.211
r_nbtor_refined	0.195
r_nbd_other	0.176
r_symmetry_vdw_other	0.146
r_symmetry_hbond_refined	0.131
r_symmetry_vdw_refined	0.118
r_nbtor_other	0.089
r_chiral_restr	0.078
r_metal_ion_refined	0.049
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	2654
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	30

Software

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