2RAH | pdb_00002rah

Human FDPS synthase in complex with novel inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZW5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	298	0.2M Ammonium sulfate, 15% isopropanol, 15% ethylene glycol, pH 4.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.171	α = 90
b = 111.171	β = 90
c = 70.44	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	MARMOSAIC 325 mm CCD	mirror/slit	2005-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	35.2	87.43	0.04	17.55	8.6	26598	26598			38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.1	57.9		0.2	6.2	4.2	2360

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		THROUGHOUT	1ZW5	2	35.2	26558	26558	1355	87.35	0.22	0.219	0.217	0.21	0.258	0.25	RANDOM	46.028

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]
-2.43			-2.43		4.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.947
r_dihedral_angle_4_deg	20.279
r_dihedral_angle_3_deg	18.624
r_dihedral_angle_1_deg	9.811
r_scangle_it	5.375
r_scbond_it	3.679
r_mcangle_it	2.325
r_mcbond_it	1.469
r_angle_refined_deg	1.188
r_nbtor_refined	0.324
r_symmetry_hbond_refined	0.258
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.207
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.092
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2780
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing