9CYZ | pdb_00009cyz

Crystal structure of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL02134

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	295.15	0.085 M tri-Sodium citrate (pH 5.6), 0.425 M Ammonium sulfate, 0.85 M Lithium sulfate, 15% (v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.75	α = 90
b = 110.75	β = 90
c = 77.5	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	RAYONIX MX-300		2016-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.3	55.09	99.6	0.046	0.05	0.016	28.4	9.7		21853			56.757

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	99.5		1.043	1.155	0.352	3.2	9.8

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 (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	FOURIER SYNTHESIS	THROUGHOUT	2.302	55.086	21810	1130	99.475	0.17	0.1704	0.1681	0.1747	0.2132	0.2188	Random	71.803

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]
-4.807			-4.807		9.614

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.763
r_dihedral_angle_3_deg	14.436
r_dihedral_angle_2_deg	10.402
r_lrange_it	8.228
r_lrange_other	8.227
r_scangle_it	6.369
r_scangle_other	6.368
r_dihedral_angle_1_deg	6.249
r_mcangle_it	4.463
r_mcangle_other	4.462
r_scbond_it	4.366
r_scbond_other	4.365
r_mcbond_it	3.118
r_mcbond_other	3.109
r_angle_refined_deg	1.627
r_angle_other_deg	0.521
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.236
r_nbtor_refined	0.196
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.166
r_symmetry_xyhbond_nbd_refined	0.157
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.015
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2675
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing