4N6O | pdb_00004n6o

Crystal structure of reduced legumain in complex with cystatin E/M

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4AW9	4AW9, 4N6L
experimental model	PDB	4N6L	4AW9, 4N6L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	25 % PEG 4000, 100 mM MES pH 6.5, 200 mM potassium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.58	α = 90
b = 85.55	β = 94.61
c = 58.92	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 315r		2013-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	48.39	99.9				40857	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	4AW9, 4N6L	1.8	44.48	2	40857	38725	2041	99.77	0.20977	0.2087	0.2087	0.21	0.2307	0.24	RANDOM	24.407

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]
-0.24		0.76	-0.96		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.573
r_dihedral_angle_4_deg	17.244
r_dihedral_angle_3_deg	11.657
r_dihedral_angle_1_deg	5.284
r_long_range_B_refined	3.239
r_long_range_B_other	2.866
r_angle_refined_deg	0.946
r_mcangle_it	0.89
r_mcangle_other	0.89
r_angle_other_deg	0.672
r_scangle_other	0.672
r_mcbond_it	0.476
r_mcbond_other	0.476
r_scbond_it	0.369
r_scbond_other	0.368
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3008
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	72

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling