4N6M | pdb_00004n6m

Crystal structure of human cystatin E/M produced in LEXSY

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	22 % PEG 8000, 100 mM MES sodium salt pH 6.5, 200 mM ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.71	α = 90
b = 82.63	β = 112.81
c = 43.49	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	2.3	41.3	95.5				10699	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	2.33	2.45	96.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 4N6L	2.9	40.12	2	5266	262	95.34	0.26175	0.2607	0.26067	0.26	0.28346	0.28	RANDOM	33.574

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]
6.07		1.72	-4.32		-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.858
r_dihedral_angle_4_deg	14.985
r_dihedral_angle_3_deg	11.969
r_dihedral_angle_1_deg	5.137
r_long_range_B_other	2.762
r_long_range_B_refined	2.761
r_mcangle_it	1.256
r_mcangle_other	1.255
r_angle_refined_deg	0.814
r_mcbond_it	0.653
r_mcbond_other	0.653
r_angle_other_deg	0.603
r_scangle_other	0.525
r_scbond_it	0.192
r_scbond_other	0.191
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1813
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	5

Software

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