3KYD | pdb_00003kyd

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y8Q	PDB ENTRY 1Y8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		279	22% PEG 2000 MME, 0.2 M di-ammonium tartrate, 3% EtGly, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.717	α = 90
b = 115.608	β = 90
c = 90.837	γ = 90

Symmetry
Space Group	P 21 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	ADSC QUANTUM 315		2008-10-27	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2008-11-09	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9790	APS	24-ID-C
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9790	APS	24-ID-C

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	2.6	25	99	0.074	15.8			33019

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)
1,2	2.6	2.67	96.1		0.367	2.7

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 (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 1Y8Q	2.61	25	32957	1673	98.91	0.23	0.227	0.2259	0.284	0.2884	RANDOM	22.961

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]
0.47			-2.72		2.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.978
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	15.472
r_dihedral_angle_1_deg	4.23
r_angle_refined_deg	0.897
r_scangle_it	0.605
r_scbond_it	0.352
r_mcangle_it	0.337
r_mcbond_it	0.181
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6724
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	39

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection