9CZ4 | pdb_00009cz4

Crystal Structure (I) of human farnesyl pyrophosphate synthase in complex with a cryptic pocket ligand, CL03049

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295.15	0.08 M Sodium acetate (pH 4.6), 0.16 M Ammonium sulfate, 20% (w/v) PEG 4000, 20% (v/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.04	α = 90
b = 111.04	β = 90
c = 73.98	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		2014-09-14	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	2.4	49.66	99.4	0.051	0.058	0.021	17.5	7.2		18514			63.164

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	2.4	2.46	99.1		0.948	1.103	0.402	1.8	7.4

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.4	49.659	18491	920	99.227	0.186	0.1828	0.2039	0.2416	0.2605	87.403

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]
-6.028			-6.028		12.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.927
r_dihedral_angle_6_deg	14.697
r_lrange_it	11.335
r_lrange_other	11.335
r_scangle_it	8.897
r_scangle_other	8.895
r_mcangle_other	6.359
r_mcangle_it	6.355
r_dihedral_angle_1_deg	6.3
r_scbond_it	5.982
r_scbond_other	5.98
r_dihedral_angle_2_deg	5.765
r_mcbond_it	4.239
r_mcbond_other	4.239
r_chiral_restr_other	3.281
r_angle_refined_deg	1.629
r_angle_other_deg	0.618
r_symmetry_xyhbond_nbd_refined	0.242
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.195
r_symmetry_nbd_other	0.192
r_nbd_other	0.154
r_symmetry_nbd_refined	0.102
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.074
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2676
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	71

Software

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