1QYM | pdb_00001qym

X-ray structure of human gankyrin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N1I	SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)
experimental model	PDB	1N0R	SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)
experimental model	PDB	1MJ0	SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)
experimental model	PDB	1N0Q	SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	3.5M Na Formate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
5.15	76.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.373	α = 90
b = 116.373	β = 90
c = 74.399	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	MARRESEARCH	mirrors	2003-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	1.0000	BESSY	14.2

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	2.8	20	99.8	0.072	0.072	35.4	13		12978

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	2.8	2.9	99.3		0.62	0.62	4

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)	2.8	20	12144	632	98.01	0.18748	0.19	0.23349	0.24	RANDOM	27.566

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]
-1.74			-1.74		3.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.897
r_scangle_it	2.205
r_angle_refined_deg	1.281
r_scbond_it	1.224
r_angle_other_deg	1.037
r_mcangle_it	0.729
r_mcbond_it	0.375
r_symmetry_vdw_other	0.29
r_nbd_other	0.243
r_symmetry_hbond_refined	0.23
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.141
r_nbtor_other	0.082
r_chiral_restr	0.067
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1680
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing