2HKE | pdb_00002hke

Mevalonate diphosphate decarboxylase from Trypanosoma brucei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FI4	PDB ENTRY 1FI4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	22% PEG 8000, 180mM ammonium sulfate, 100mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.463	α = 90
b = 168.666	β = 118.78
c = 54.85	γ = 90

Symmetry
Space Group	P 1 21 1

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	mirrors	2004-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	ESRF	ID14-4

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	1.8	42.18	99	0.106	0.106	4.3	6.1	74800	74805	2	2	24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.9	98		0.658	0.658	1.1	5.8	10804

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	PDB ENTRY 1FI4	1.8	42.18	74800	74800	3767	98.96	0.168	0.168	0.166	0.1758	0.208	0.2149	RANDOM	24.335

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]
-0.81		-0.82	1.02		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.965
r_dihedral_angle_4_deg	18.041
r_dihedral_angle_3_deg	14.062
r_dihedral_angle_1_deg	6.161
r_scangle_it	3.897
r_scbond_it	2.776
r_mcangle_it	1.595
r_angle_refined_deg	1.558
r_mcbond_it	1.413
r_angle_other_deg	0.922
r_mcbond_other	0.263
r_symmetry_vdw_other	0.233
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.21
r_nbd_other	0.198
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.095
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_xyhbond_nbd_other	0.013
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	5820
Nucleic Acid Atoms
Solvent Atoms	712
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALA	data scaling
AMoRE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction