2IQ1 | pdb_00002iq1

Crystal structure of human PPM1K

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	294	100mM Hepes pH 8, 18% PEG 10K, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.442	α = 90
b = 69.406	β = 90
c = 77.401	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	CCD	MAR CCD 165 mm		2006-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	2.25	51.674	99.9	0.147	0.147	15.7	7.8	15773	15758			38.4

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)
	2.25	2.37	100		0.848	0.848	2.5	8	2247

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.25	20	15718	15717	785	99.99	0.184	0.181	0.1837	0.239	0.2395	RANDOM	51.645

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]
2.4			-0.02		-2.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.462
r_dihedral_angle_4_deg	20.207
r_dihedral_angle_3_deg	16.621
r_dihedral_angle_1_deg	6.576
r_scangle_it	4.558
r_scbond_it	2.822
r_mcangle_it	1.707
r_angle_refined_deg	1.557
r_mcbond_it	1.012
r_nbtor_refined	0.301
r_symmetry_hbond_refined	0.217
r_nbd_refined	0.201
r_metal_ion_refined	0.193
r_xyhbond_nbd_refined	0.141
r_symmetry_vdw_refined	0.136
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1992
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing