6VMT | pdb_00006vmt

Leishmania major Programmed Cell Death Protein 5 Homolog

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6IQO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	300	1.5 M K2HPO4

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.386	α = 90
b = 115.386	β = 90
c = 58.628	γ = 120

Symmetry
Space Group	H 3 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	ADSC QUANTUM 315		2005-03-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.95373,0.97962,0.97949	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.5	25.296	87.8	0.114	0.122	0.04	0.998	11.3	8.9		4643

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6	53.5		6.236	6.752	2.424	0.264		6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6IQO	2.501	25.296	4640	194	87.829	0.224	0.2223	0.2727	79.593

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]
-0.435	-0.218		-0.435		1.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.103
r_dihedral_angle_4_deg	20.708
r_dihedral_angle_3_deg	20.702
r_lrange_it	17.389
r_lrange_other	17.382
r_scangle_it	14.901
r_scangle_other	14.887
r_mcangle_it	9.843
r_mcangle_other	9.834
r_scbond_it	9.396
r_scbond_other	9.385
r_mcbond_it	7.567
r_mcbond_other	7.344
r_dihedral_angle_1_deg	5.778
r_angle_refined_deg	1.605
r_angle_other_deg	1.262
r_symmetry_nbd_refined	0.258
r_nbd_other	0.227
r_nbd_refined	0.222
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.154
r_nbtor_refined	0.153
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.06
r_bond_refined_d	0.01
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	783
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MoRDa	phasing